Mass Effect 3/Headscratchers

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Detecting Reaper on Ranoch
Normandy is equipped with IFF device, in the Mars mission it is shown that EDI is capable of "detecting Reaper presence". Then why is it that no one is aware that a Reaper is present on Ranoch? There are a lot more questions about IFF, like how the Salarian are able to equip their dreadnought with IFF but human can't (considering it is on the Normandy), but I just like to know how Normady couldn't detect Reaper presence on Rannoch.
 * The Rannoch Destroyer could have been in some kind of "silent mode" to keep it from being detected until Shepard and co. got close enough to tag it with the targeting laser. Also, there were geth jamming towers all over the area that could have made detecting it from orbit more difficult.
 * Reaper IFF does not allow one to detect Reapers. It lets one masquerade as one to defeat the Omega-4 Relay. Also, the Reaper was deep underground and not active, whereas the ones over Mars were moving and putting off massive emissions that could be easily detected. Its the difference between using a thermal scope to spot a moving vehicle through its hot engine and using it to try to find a vehicle whose engine is not active and still cold.
 * So, a Reaper can become inactive yet still be able to send signal to control the whole Geth armada?
 * A truck can shut off its engine while still being able to send radio transmissions.
 * On Mars, the Reapers weren't trying to hide; you could look out the window and see them. On Rannoch, the Reaper in question was hiding under an entire Reapertech military base.

Cerberus power level discrepancy between Mass Effect 2 and Mass Effect 3
Seriously, I know it's because they're villains now and we need something to fight that isn't husks or giant floating spaceships, but where were the giant mechs and legions of commandoes in Power Armour when Shepard was fighting for his/her life in Mass Effect 2?
 * They had you, who repeatedly be proved to be more than enough. Why send a platoon of soldiers when a hypercompetent team of 3 will get the same results. Likely, if you never got around to something, they'd have sent their armies later.
 * Cerberus had the resources and manpower to:
 * 1) Build Project Overlord, which involved multiple geothermal power stations, a large above-ground facility including an immense satellite uplink station bigger than the satellite in Golden Eye plus an underground facility almost as big,
 * 2) The Derelict Reaper operation, which involved extensive construction of platforms and equipment transportation
 * 3) Project Firewalker, which also developed an entirely new ground combat vehicle (much more expensive that it sounds)
 * Well, according to a discussion between James and Cortez, the Hammerhead was an Alliance tank model originally. I don't remember what the codex said, however.
 * 1) The Lazarus Project, which required its own dedicated space station, on top of the resources poured into Shepard, which in his/her own words, "You could have trained an army for what you spent on me."
 * 2) Rebuilt the Normandy, one of the most expensive and advanced warships in the galaxy, which cost as much as a heavy cruiser or twelve thousand fighters, and then improved on the design.
 * 3) Subsequently supported and funded the Normandy during Shepard's romp across the galaxy.
 * 4) Operated numerous R&D projects to develop Cerberus Assault Armor, Inferno Armor, the Arc Projector, the Eviscerator, and modified the Mattock, on top of research into geth weapons.
 * 5) Maintained a space station solely for the Illusive Man that moves every time anyone of his agents visits the station.
 * 6) Suffered raids by Hierarchy troops on a dozen of their projects and installations in Retribution, without being seriously hampered
 * 7) Maintained combat operations in several areas in the Terminus with platoons of commando troops
 * 8) This does not factor in various other projects and operations, such as their extensive intelligence network and legal apparatus.
 * With all of these projects they've been able to fund and operate, you're somehow having a hard time wrapping your head around them maintaining a few mechs and a battalion of infantry? If anything, the question here should be the discrepancy between Cerberus' resources in ME1 and ME2.
 * I think the question is actually the opposite of that -- not so much "how can Cerberus afford this" but "why didn't they use these things in Mass Effects 1 and 2, since they're so rich anyway?"
 * Primarily because Cerberus was largely covert in the first two games, hiding their strength and so on. They were engaging in some combat operations in the Terminus (you get as much from the messages TIM sends you whenever you get some DLC equipment). However, clearly something has changed in the Cerberus leadership/goals if they're changing their gameplan this drastically. Indoctrination is one of the better explanations.
 * Just to nitpick, the Hierarchy raids in Retribution actually did cripple Cerberus... in the Terminus Systems (which was why the Illusive Man needed to get Aria to help him). Everything we've seen of Cerberus in Mass Effect 3 so far indicates they're still an NGO Superpower in Citadel/human space, however.
 * Perhaps
 * The most likely explanation is that yeah this stuff was around in the first place, but in Mass Effect 1 they were trying to be covert, and in Mass Effect 2, it was better for Shepard and co to be discrete, but in Mass Effect 3, top brass has gone nuts and it's all out war, so hiding your best cards really doesn't do you any favors.
 * According to Bioware, figuring out how Cerberus has suddenly acquired so much war material is a plot point. So it will be dealt with at some point.
 * But according to EDI, Cerberus has 150 operatives. Somehow, these big strike teams don't seem to gel with a number that small.
 * Depends how Cerberus defines "operative."
 * "Operative" Lawson. Miranda is only one person.
 * That's exactly the point. Miranda was in charge of her own team and had numerous personal working under her. Every "operative" could have the same.
 * There's also a chance that EDI didn't have correct/complete information. It wouldn't be strange at all for TIM to keep certain stuff well under the radar.
 * EDI explicitly says that each cell is commanded by an operative. So we're looking at potentially 150 cells with comparable manpower to the Normandy operation, which is consistent with Cerberus' resources.
 * Mass Effect 2's Codex entry on cerberus mentions that they've recently shifted focus from covert operations to stockpiling weapons, ships, and recruits and conducting more overt operations. This may reflect how they've shifted their efforts and gained so much combat capability in ME3.
 * Actually, it makes sense if you pay attention to Cerberus' deployed forces. Cerberus' troops almost always consist of infantry platoons backed by light armor in the form of Atlas mechs. They have some spacecraft, but a comparatively limited amount. Their real strengths are in what effectively amounts to large numbers of air-mobile infantry backed by light armor and air support. This makes sense when you take Sanctuary into account; Cerberus has likely been abducting, recruiting, or coercing ordinary people, whammying them with indoctrination and implants and turning them into soldiers. Once done, they equip them with infantry weaponry and armor and deploy them in commando units to assault sites and hold them temporarily before withdrawing. Outfitting infantry in this setting shouldn't actually be that hard or expensive, considering established industrial capabilities. They can't maintain long-term occupation - their efforts to control Benning and Eden Prime and even temporarily control the Citadel shows this much - but Cerberus can hit and run. And that's largely what they do.
 * And midway through the game we get an answer as to where they were getting a lot of their stuff:.
 * And later, we learn how they managed to increase so dramatically their manpower: : in fact, there are many hints, like the fact that on Mars   while on Sur'kesh, a wounded cerberus soldier seem unable to give any coherent answer to Shepard , during later encounters, Cerberus troops seem to become  . One mission consist of stopping them from attacking a colony: both Hackett and Shepard agree that this is different from Cerberus usual MO

Geth, paragon choice? Really?
Why they are the paragon choice? I really hated the fact that issues of the geth's genocide of the quarian during the mourning war as well as the true geth's inaction against the heretic, who are tiring to bring extintction on EVERY-SINGLE ORGANIC CIVILIZATIONS have never been brought up during the game. And the fact you can't even call the geth on the horror they did in the past make it worse. Bioware made the issues annoyingly one sided: Ah it's all the Quarian's fault, they attacked first, who cares if the geth killed billions of quarians mostly civilian and noncombatant and dooming the rest to a slow extinction on the flotilla. Why are the geth presented as innocent victims? Yah, innocent victims who killed Billions in response indiscriminately.
 * Geth's logic: We commit genocide by killing more than 99.9% of the quarian and let our splinter group bring back Reapers without taking any action. We did it in the name of self-defense and isolationism; therefore, you cannot blame us for anything, it's all the organics' fault.
 * Throughout the series the geth almost never shoot first, the quarians have a habit of trying to kill them all off which leads to the geth fighting back, but always holding off the killing blow. The original geth war was started when the geth began to show more intelligence than originally expected, and began asking philosophical questions about themselves. The quarians' response to this was to attempt to wipe out the geth in their entirety. The geth fought back and defeated the quarians, once they had done this they had both the means and a strong motivation to finish the job and kill all remaining quarians, but they chose not to and instead withdrew from organic-controlled space and didn't bother anyone for the next 300 years. The geth that served Sovereign were a tiny splinter group, and the rest of the geth did try to do something about it, that's what Legion's loyalty mission was all about; if their actions justify extermination of the entire species then what do Cerberus mean for humanity? Finally, the geth in Mass Effect 3 were only pushed back into supporting the Reapers after the quarians attacked them yet again. The whole conflict could have been avoided if the quarians were a bit less trigger happy.
 * Trigger happy? Is that what you call wanting their homeland back? To no longer depend on their suits?
 * When the galaxy is being invaded by armadas of mecha-Cthulhu at the time? Yes.
 * You are making the common mistake of assuming "Paragon = good." Paragon isn't good, its idealistic. Paragon Shepard views the geth as innocent victims in the current point in time, as the geth were directly attacked by the quarians when the galaxy needs to be united against the Reapers. Shepard is, honestly, mature enough to decide that what happened three hundred years ago needs to be let go and everyone needs to focus on the real issue. And when it comes down to it, Paragon Shepard is willing to side with the species who, in the current conflict, were attacked without immediate provocation over the species that launched said attack. Renegade Shepard feels differently about the whole thing.
 * Welcome to the concept of Grey and Gray Morality! Besides, regardless of where the choices are on the dialogue wheel, siding with the Geth is not the Paragon choice in that situation. The option "Rally the troops!" (which leads to peace between the geth and quarian races) is.

Vanishing Kid

 * OK, so the kid that pulls a Stealth Hi Bye in the demo: how? I understand Rule of Cool and Rule of Drama, but the kid demonstrated that the airvent wasn't soundproof. That's how Shepard managed to detect the kid in the first place. Now the kid had to get around the corner fairly quickly during the few seconds Shepard looked away (he was about halfway there when talking to Shepard) and considering that couldn't be quiet while moving slowly, it seems unlikely that he could be silent while moving fast. How is it that the kid managed to get around the corner without making any noise?
 * In a noisy, chaotic environment, it'd be pretty easy for the kid to slip away before Shepard could notice if he/she took his/her eyes off him for a few seconds.
 * Seriously, Tropers! I timed it, and Shepard was looking away for 10 seconds. Isn't that enough time to move two feet?
 * Certainly. The problem is that it doesn't seem to be enough time for him to move quietly.
 * Just because the kid wasn't moving like that when we first meet him, doesn't mean he isn't capable of it. What's more important, is that game-play represents the perspective of Commander Shepard, and perception is selective. Also applies in Real Life: Did you hear your computer humming just before reading this? No, you were focused on other things. Did Shepard hear the kid moving? No, he was talking to Anderson.
 * After playing the demo, it is possible to see that the kid was at the end of the corridor, so the only was for him to continue to move was making a turn. It would take, like 2-3 seconds to get out of sight.
 * It's also possible that the kid only exists in Shepard's mind. Would explain the vanishing and why nobody at the shuttle landing site reacts to him in any way. We might see that kid later in the full game.
 * What.
 * Oh we see him later alright. In a cut scene when the shuttle he gets on is blasted out of the sky by a Reaper.
 * Indoctrination Theory, there is a chance that the kid is a hallucination caused by Shepard slowly being indoctrinated.
 * It's long, but watch this video on the indoctrination theory. It explains the little kid.
 * The indoctrination theory seems pretty unlikely now, given that the whole thing hinged on the idea that Bioware had deliberately created an unsatisfying fake ending with the intention of releasing the pre-planned true ending later. Ending DLC is on its way, but everything Bioware have said suggests that this is a response to fan outcry rather than something planned from the start (and if it was planned in advance they could just release it now rather than the vague "summer" release date), they also claim that the DLC will expand on the ending but not change it.
 * Jossed. There's a picture of the kid on the memorial wall in the Citadel refugee district.
 * Unless you/Sheppard are just imagining it is that kid.
 * Actually, during the early stages when you're learning how to fire your weapon against the climbing husks, you can actually see the boy running across the roof and into the room if you adjust the camera/your view.
 * A room that gets blown up a second later, mind.
 * You realize that Earth is being attacked by Reapers at the moment, right? Shepard's kind of got enough to distract him/her, the sounds of the explosions and fighting outside and the fact that Anderson called for him/her from another room seconds before could easily be enough noise to hide the sound of the kid moving.
 * Still, it begs the question why Shepard didn't tell Anderson "Hey, there's a kid in here! We can't leave him!" like any sensitive and reasonable human being would.
 * Because the kid is gone, and they're just fighting to stay alive at that point. Shepard and Anderson don't have time to go digging through the ductwork for the kid. They have to get the hell out of there.
 * Because the kid is gone, and they're just fighting to stay alive at that point. Shepard and Anderson don't have time to go digging through the ductwork for the kid. They have to get the hell out of there.

Normandy's Leaving Earth

 * This is just something minor, but... the first mission takes place in London, right? When the Normandy is exiting the atmosphere, it's clearly leaving from somewhere in North America. I'm preeeeetty sure London is in a completely different area of the Earth. Like, halfway around the world.
 * Isn't the first mission in Vancouver? (Perhaps as a shout-out to the Canadian-ness of both male and female Shepard and Bioware itself) ... Memory could be misleading, however.
 * Word of God is it's the future's Vancouver-Seattle megalopolis.
 * It was never said anywhere that the first mission takes place in London.
 * Just because the first promo took place in London doesn't mean the first mission took place there.
 * So... the Reapers take the time to shoot down two small and defenceless shuttles, but the Normandy, a much larger and well-defended frigate, escapes with no hassle? And don't give me any of that "Oh, stealth system!" nonsense because ME2 already proved Reaper tech can see through the stealth.
 * The shuttles probably have more people on them. The Reapers want the people to melt into goo. Besides, it's not like they have time to shoot down everything.
 * It's more than likely the Normandy's Reaper-IFF from the last game managed to hide it from the Reapers long enough to am-scray before they realized something was amiss. It's a long shot but it's the most likely explaination I can think of.
 * Not to mention we saw moments before the Reapers destroyed a Dreadnought so its likely they're going after the bigger targets first. The Normandy is also mentioned as being one of the fastest Alliance vessels in the fleet, it also spends barely two minutes before making a break for it and as noted above, combining the Reaper-IFF and their stealth systems, its likely hard to make a bead on them rapidly. In all previous cases, there was only the Normandy present and the Reapers were actively looking for them at the time. Even if they are now, there are hundreds of crafts they've got appearing on their radar to make that task next to impossible.
 * The Normandy was already leaving before the shuttles were destroyed, and afterwords the Reaper immediately turns its attention on the ground forces firing at it.

Ashley's Rank/Appearance

 * Ashley and wearing civilian clothes to testify before a military board. What, did she get kicked out, too?
 * Ashley is a Spectre now. Technically, she's not bound by any Alliance regulations at all. She can wear whatever the hell she wants, and Spectres are encouraged to be individuals.
 * Ashley wasn't a Spectre at that point; the offer hadn't even been put on the table.
 * Secondly, why and how is she a lieutenant commander? She was a Marine, so far as I could tell, in ME 1 and 2. And an enlisted Marine. And now she's an officer with a Navy rank? Let's say that she went OCS and became an officer... why is she a lieutenant commander? Kaidan (if you keep him alive) is a major. Major=lieutenant commander. But Kaidan was a lieutenant when we first met him. Which is two to three ranks below major. Whereas the hypothetical "gunnery chief," even if she went OCS, would be starting out at the lowest level of the Navy officer corps, which is going to be at least a little below whatever kind of lieutenant Kaidan was.
 * You are making the mistake of assuming that Systems Alliance rank structure is anything like real life NATO-style rank structure. Its not. SA Marines and Navy are actually the same branch, just with different focuses and terminology for ranks, and use the same rank progression. (And technically, Major is a SA Marine equivalent of Captain, or 0-6) As for getting promoted to an officer rank, Ashley and Kaidan are both Spectres, so the normal military rules no longer apply to them. They've obviously been very much fast-tracked because they're now the second human Spectre.
 * Don't forget that Shepard was a marine before becoming a commander. During Elysium/Akuze/Torfan, Shepard was an N5. It was only after that that s/he became an N7 and went into officer training. Same thing with Anderson. During the FCW, he was an N5, and by the time he went onto that mission with Saren he was an N7.
 * No. Per Mass Effect: Revelation, Anderson graduated the N7 program at the age of twenty, shortly before the First Contact War broke out. There is no reason to suppose Shepard wasn't already N7 at the time of Elysium/Akuze/Torfan, either.
 * According to the concept art book, Ashley's outfit is not civilian clothing at all, but apparently an officer's outfit. Why it looks different than the female officer outfits that say, Fem Shep or Kahlee Sanders wears isn't explained.
 * Modern militaries have different classes of uniforms for different occasions. It wouldn't be that unusual for the Alliance to do the same.
 * What bothers me is the usage of "Lieutenant" as a short form for her rank, which is completely wrong. It should be "Commander", like Shepard before her promotion. I think there is an out-of-universe reason for this, however. Early articles reported that Williams would be a Lieutenant in ME 3. I suspect some of the lines were already recorded when they changed her rank.

No Turian Infiltrators in muiltiplayer?

 * Why can't you play a Turian Infiltrator in multiplayer, even though one of the most popular Turians in the series is one? And while we are on the subject, no Krogan Vanguards? Seriously?
 * Said turian and krogan are mavericks among their people.
 * Wrex is a Krogan Battlemaster. He's extremely rare among his people, because he needed to be exposed to Eezo before birth. Yeah, he was born before the Genophage, but even before then, Natural Krogan Biotics were rare.
 * The Krogan Sentinel's biotic powers come in the form of biotic grenades, so yeah, as awesome as a Krogan Vanguard would be, it's going to be at best a really rare drop. On the potential plus side, we might get to see Quarian Sentinels.
 * No Quarian Sentinels. Likely it's just because a Krogan Vanguard has the potential to be stupidly broken. Krogans and Vanguard are already fairly broken.
 * Well, part of the OP's wish has been granted. Krogan Vanguards are to be released in free DLC on April 10th. How overpowered they will be has yet to be seen.
 * Not Original Poster but SQUEE!!!
 * And the answer to how overpowered they are is "very." This troper is an average player at best and has (on Bronze, at least) finished with the highest score on my team EVERY TIME I've played my Krogan Vanguard. This troper thinks the only reason he even carries a weapon with that guy is for the bayonet on the shotgun.

Quarians and Geth

 * Read on, but you have been warned, why is helping Legion the paragon option? Yes, I know he's trying to make his people independent, but that's using Reaper Programs, it's a terrible idea! And your only options are killing the Geth or the Quarians? There might be other options if you had brought Legion to the fleet in ME2, but from what I've seen, I heavily doubt that. And this is coming from footage- not a leaked script. The worst part about this is it ends in Tali's suicide... Why is this the only option!?
 * Its not. There are multiple ways that the issue between the geth and quarians can be handled. Determining whether you can create peace between the two runs on a seven "point" scale: you get three points in ME2 (two for destroying the geth heretics, one for having a loyal surviving Tali to become an admiral) and four more points based on your actions in ME3. However many points you earn in this regard determines how easy it is to broker a peace between the two.
 * Correction: Actually, you get two points for destroying the geth heretics, two points for preventing the Quarian fleet from exiling Tali, 1 point for resolving the dispute between Tali and Legion in ME2, and 1 point each in ME3 for respectively . You need at least 5 points in total to ensure that the quarians and geth will work together to help you fight the Reapers.
 * You should do more research before (metaphorically) screaming your head off; this video shows what happens if you Take a Third Option:
 * There is no hint of any of this in-game; if you don't have it unlocked there are no persuasion options and wiping out the Quarians is in the usual Paragon spot.
 * No hint? This isn't a puzzle to get the blue key, it's solving a hundred years+ war between the species, and you're talking like they should hand you the option to get the perfect crispy clean ending outlined in a step by step process in the codex? No crap they don't give you a hint, it's not called Earn Your Happy Ending for nothing!
 * I'm glad someone took he time to mention that. Why would it be easy to bring peace to two species where one of them tried to exterminate the other? You'd need to pay attention and look at who would support you, who would not, and how you can take the least damaging path to your solution.
 * Taking out the fact that there's a third option, siding with the Geth makes sense as the Paragon choice. The Geth did nothing wrong, they were just created. The Quarians chose to exterminate them before even giving them a chance and the Geth had to defend themselves. Even after the war, the Geth did not take over the Quarian planets, but maintained them for their Creator's eventual return. The Quarians draw some parallels to the Reapers as they are trying to exterminate a species before that species even has a chance to make a mistake, much less learn from it. Makes sense that the Quarians are the renegade choice, as they choose extermination over preservation of life (even synthetic life).
 * But again, the Geth plan to upgrade themselves using Reaper Programs That is an incredible risk and every single time a species has tried to use the Reapers for personal gain, it's backfired. Shepard knows this.
 * And how does that make that decision any less of a "paragon" one? Paragon Shepard has always defended the helpless against the aggressor. There's no room for black and white "Well you tried to use Reaper Programs while being attacked so I'm going to let you be destroyed while you can't fight back". Allowing the Quarians to completely destroy another sentient species due to a one-sided account of a situation they (The Quarians) caused would not gain you Paragon points.
 * They're using Reaper code to enhance themselves. This is both out of character for the geth, as explained to us by Legion in ME2 (the whole purpose of the geth/heretic schism was that the heretics wanted to use technology from the Old Machines to fasttrack their evolution process) and for Shepard, who has never accepted using reaper tech to fight them before. It's shoddy writing at best, and High Octane Nightmare Fuel at worst.
 * It's worth noting that that not all of the Quarians wanted to fight the Geth, even if it mainly came from trepidation instead of feeling empathy for the Geth. Admiral Gerral (and, to a lesser extent, Admiral Xen) was the only one aggressively wanting to destroy the Geth at all costs. Admiral Koris and Tali were very ambivalent, and it's easy to get the impression that the other Quarians only followed through with Gerral's orders out of desperation to get back to [their homeworld] Rannoch, rather than malice towards the Geth. Also, during the Geth's memories of the 300 year war starting, a minority of Quarians were Geth sympathizers that suggested peace and negotiations instead of the knee jerk reaction most of them wound up doing. Both sides of the conflict have major baggage towards the other, and yet, neither race deserve to destroy the other out of a massive misunderstanding. No matter the choice, one side will undeservedly get massacred from a pointless war which started from a huge misunderstanding. It's the most heart wrenching Grey and Gray Morality choice of the entire series for these reasons.
 * With the Reaper Code thing, what people seem to overlook is that the Geth were disorganised after the Reaper's death, and the Quarian fleet was using that to try and wipe them all out. Legion isn't out of character for taking the only action that would prevent the genocide of his people; he even spells it out for you that if he didn't use the Reaper Code the Quarians would destroy his people. As for Reaper tech never having positive effects; EDI was reversed engineered from Reaper Tech, and she's a valued member of the Normandy.
 * This still doesn't explain why letting Legion upload the code was a "Good" option. There should have been an option to talk the quarians out of attacking the geth that doesn't leave us with potentially huskified geth.
 * You try to talk the Quarians out of it on multiple occasions. Virtually every mission you undertake in the Rannoch arc is supposed to buy them time to withdraw from the war, but Gerrel's single-minded mania keeps him from doing it - he seizes every opportunity to press the attack, even at the risk of killing Shepard and Tali.
 * So why do we never get the chance to call What the Hell, Quarians for conveniently forgetting their extermination of the geth-sympathetic Quarians during the uprising? Sure, it's their ancestors who did it, but you'd think they'd have learned by now.
 * It's kind of pointless by this point. They had been forgotten and as you said, it was their semi-distant ancestors who did it.
 * Because there's no point. At this point, its like a Frenchman calling out a Brit for something that happened during the Hundred Years' War. Everyone involved at that point is long since dead and its long since been forgotten.

Casual Outfits Beyond The Normandy

 * Serious Shepard, why did you stop wearing armor and packing heat inside the citadel nowadays? Ah remember during Thane's loyalty mission where you reported vermin as citadel health inspectors? Packing a plethora assault weapons to deal with rats. Now you just travel in regular clothing without even a sidearm.
 * The better question is why Shepard was packing armor and a personal armory while walking around the Citadel in the first two games. The Citadel generally didn't need them, and as of ME3 Shepard doesn't engage in any combat on the Citadel at all. That said, Shepard likely has a sidearm concealed on his/her person underneath his/her clothes; if Shepard can slip a heavy pistol in underneath a fairly-tight-fitting tux/cocktail dress, s/he can conceal a sidearm in regular clothes.
 * Actually he does not have one, as he needs to borrow a pistol from one of the Blood Pack vorchas to take out a corrupt contact for Aria.
 * Shepard is constantly armed, though. He/she has his/her omniblade.

Ending

 * Why are people complaining about how the destruction of the relays means the end of galactic civilization? The FTL communications network is separate from the relays, so people will at least be able to talk to each other across the galaxy; everyone still possesses mass effect technology, so even though inter-stellar travel will be slower without the relays it should still be possible; and of course they could always build more relays, especially if the Reapers decide to help rebuild the galaxy in the synthesis ending.
 * Comm buoys were destroyed by the Reapers, only QEC could be used. You also vastly underestimate the size of the galaxy. The Normandy couldn't even traverse a cluster without stopping to top off, and the garden worlds are so far away that galactic civilization wasn't feasible without mass relays.
 * Actually the comm buoys that where destroyed/lost only happened in Batarian/Human space, no evidence has been shown to say that the galaxy wouldn't be able to communicate, aside from the Batarians, which, lets face it, the only ones left are outside Batarian space anyway, because by all logic, they should all be dead.
 * At the time, only Earth and Batarian space had been attacked. You think they wouldn't destroy the comm buoys in Asari space once they enter Asari space? And by the end, the Reapers are in every system with a mass relay. If they took pot-shots at Bekenstein, surely they would take pot shots at the comm buoys.
 * Without the Mass Relays, we've gone from 20th century mass transport with relays able to take you anywhere in the galaxy within a couple of days, most of which is spending waiting your turn at the relay, to 19th century slow communication, ships taking weeks to cross the Atlantic. Galactic civilisation will no doubt need to adjust, but it can recover from this - not to mention that relays can be rebuilt!
 * Once again with the vastly underestimating the scales involved. The Normandy can't even cross a cluster without refueling, and these are just within tens of light-years of mass relays. The galaxy is 100,000 lightyears across, and the races are spread out in little clusters across the entirety of that 39,000,000,000,000 cubic lightyears. Unless Bioware says that standard FTL can travel at hundreds of thousands of times the speed of light, "weeks" won't cover it. Say my Asari war assets want to get home. From the positions on the galaxy map of Thessia compared to Earth, and given the size of the galaxy, I'd estimate at least 25,000 lightyears. To do that in 3 weeks, you would have to travel at a staggering 470,000,000,000,000 km/h, or 435,000 times the speed of light. For comparison, at those speeds I could hop out to Alpha Centauri in 5 minutes (not counting acceleration and deceleration, but the Normandy appears to hit max speed pretty quickly in its intra-cluster FTL jaunts), or Mars in 1-3 milliseconds (depending on which side of the sun it's on relative to Earth).
 * Further, it took the reapers 6 months at FTL to get from the Bahak system (Alpha Relay) to Earth by going to the nearest relay and then using it to get travel quickly to Earth. Even considering that they probably stopped off to harvest the Batarians, most of that time still had to have been transit otherwise someone would have wondered, "Why have the Batarians been out of contact for a month?" If the Reapers, far more advanced in FTL than the citadel races, took even 4 months just to get from one relay to the next closest, the Citadel races have no hope of seeing home again before their fuel and supplies run out.
 * One more point: The Codex for the Mass Relays notes that "[Mass Relays allow] instantaneous transit between locations separated by years or even centuries of travel using conventional FTL drives." This should be sufficient in-universe lore to show that "we've gone from 20th century mass transport" to "amoebas attempting to swim against the current from Cuba to Africa."
 * Actually, FTL comms is made possible by the Mass Relays for communication beyond the cluster. Link if you doubt me. Since Sol is the only system that uses the Charon Relay, the only way to get a signal from Earth to basically anywhere else in the Galaxy is with a QEC. Too bad that two of the half pairs on Earth now lead to nowhere, since they were probably destroyed in the Normandy crash, along with lord knows how many other half pairs. Also, it's too bad that QEC's are expensive and rare and most likely limited to military vessels - a good chunk of whom were destroyed trying to retake Earth. Long story short: you might be able to phone up someone the next system over, a few parsecs max, but anything further will effectively be snail mail.
 * Why does the Catalyst look like the ghost of Disappeared Kid?
 * A Form You Are Comfortable With. Considering the nature of the Catalyst, it likely did something similar to what Javik does to analyze the mind. The "less" advanced Protheans could do something similar with their beacons. It likely appeared as the child to further galvanize Shepard into making the decisive decision.
 * How does having a bigger fleet affect what setting off The Device does?
 * More war assets likely mean that Shepard suffers less of an overall beating while getting to the Catalyst in the first place. Also keep in mind that the Catalyst is offering these options freely as solutions because organic life fought hard enough to get to that point. Presumably, it tailored the solutions to reflect that.
 * What needs to be considered is that many war assets contribute towards the development of That Device. This would be the logical reason as to why.
 * Why does Shepard not argue about the inevitability of a synthetic war even after siding with the Geth or forging a lasting peace? It fits with ideas from the first game about coexistence being impossible, but Legion convincingly argued against that in the second. Every violent AI in the series other than the Catalyst itself was driven to it by panicking organics trying a first strike on the assumption it would rebel, even when it just tried to ask questions.
 * There's not really a point to arguing about why. There's a battle raging right outside. Maybe if Shepard was just sitting down with the catalyst AI at a card table, they could argue the merits of its viewpoint, but as it is, Shepard really doesn't have time to debate the finer points of synthetic/organic relations when every second s/he spends jabbering with the Catalyst is another ten thousand or so people dying while fighting the Reapers. Philosophy and motivation can go out the airlock; Shepard has a job to do.
 * Yes, the moment when the fate of the galaxy is being decided is clearly not the right time to make sure that all the options have been considered so the right choice can be made.
 * At this point in time though, the "right choice" is about which way is the best way to beat the Reapers there and then. the wider philosophical reasonings as to why synthetic life forms will always turn on their organic masters will not affect this decision
 * Shepard ALWAYS takes time to stop and argue all through the trilogy.
 * Not really. Shepard only takes the time to stop and argue when s/he needs information from the person s/he is arguing with, or if s/he needs to stall for time, or if there's no harm in stopping briefly to try to convince someone to change their opinions. Both his/her arguments with Saren and Harbinger were due to waiting for the Normandy to pick him/her up, while the argument with Saren at the end of the first game was to cut short a confrontation. The Catalyst is different. Arguing with it won't get anywhere, especially when thousands of people are dying every second to give Shepard this chance. Victory is right there in front of Shepard.
 * Really? There's no reason to try to talk around the guiding intellect behind the Reapers, to attempt to convince him to call them off, especially when he's so obviously wrong it hurts?
 * In case you did not notice: Shepard is bleeding to death: s/he managed to survive a direct hit from Harbinger, to succesfully reject the indoctrination process during the showdown with the illusive man, all of which is very impressive, but that's it: Shep's plot armor is gone and s/he's living their last minutes. In fact, it's quite clear that Shepard was about to lose consciousness for good after the last dialogue with Anderson: sure, an healthy Shep may have started a debate with the catalyst, maybe even reached a compromise, something like "leave now, come back next cycle and see if we managed to destroy ourselve during your 50.000 years interegnum''. The problem is, Shepard is at this point dying and in no state to do anything but to choose one of the catalyst solutions and limp toward it.
 * Its a millions-years old AI on an implacable, unstoppable fleet of super warships. It is also offering you a solution to the entire mess, no strings attached. Shepard doesn't need to argue with it, as s/he's already won, Shepard just needs to choose how to win.
 * You call that "winning"? Seemed like a lose/lose/ scenario to me. You wanna talk about picking how to win? How about pointing to the Geth and Qurians co-existing, something I worked my ass off and sacrificed a friend to make possible, and saying to that fucking Catalyst "you're wrong, fuck you."
 * He is wrong! He comes just short of outright admitting he's wrong! That's why he's standing to the side instead of fighting you!. There is no other way to win, because the Reapers won't stop until you activate the Crucible! Welcome to war, the winner is the side is less devastated!
 * I'd wager a few Shepards would rather fight this forced-attempt-to-appeal-to-sympathy character avatar one-on-one (ala Gurren Lagann) or engage it in a battle of wills than being constrained to three choices that change the colour of the ending cutscene. At least it'd be a path they choose for themselves, not handed to them by this "Catalyst" as an illusion of choice (besides, it'd feel oh so satisfying proving it wrong by actually managing to beat the Reapers conventionally anyway despite all odds). We already have a grim depiction of the brutalities of conflict in the form of DA 2, MW and DE:HR, do we really need to have it shoved down our throats here too?
 * It was an all-way lose to me, too. Fridge Logic just tells me that if the Relays exploded then a lot of homeworlds just got wiped out. Including Earth. Normandy, being the fastest non-Reaper ship, was probably the only ship able to escape the blast relatively intact, thus giving the "best" ending of synthesis where Joker and EDI can be together. Yay. Never mind all those other people, they're all dead, go meet Garrus at the bar. Of course, then there's the Kill The Reapers Ultimate version where Shepard apparently somehow survives, so maybe Earth didn't get wiped out (but then why is Normandy escaping random blast?). I don't know, none of it made a lot of sense to me. It felt almost like Catalyst had just concluded an utterly insane The Plan in which Shepard always loses. The best Shepard could do was make sure some people survived, but ultimately every solution would end with the complete collapse of galactic society. Heck, I shot the conduit out just because I felt after all the crap the Reapers have pulled in their Evil Plan it was the only sensible thing to do (Like the illusion that the Reapers can be controlled to create infighting and the subtlety of indoctrination, Mass Relays to force technology along a certain line, etc. Like everything they give you that you think might help you win against them is just another part of their plan to destroy you). Even this felt like a loss because of the Geth and, presumably, EDI (not to mention sweeping parts of the galaxy potentially).
 * To me, what it boils down to is that you can argue with a gun all you want, but even assuming the gun can argue back, there's a limit to what it can do; fire. Any argument Shepard can throw at the catalyst is countered by "Look. These are the options. It isn't a philosophical debate, this is what is physically possible for the crucible to do. Pick one and run with it." It's better explained in the original script which included more exposition, where the Catalyst explains that the crucible altered it's function to the point that it no longer has direct control over the reapers.
 * Satisfying though it may be to beat the Reapers conventionally, if that were actually a possibility, the Crucible wouldn't have been necessary in the first place. More often than not, the odds being stacked against you doesn't mean "heroic victory at the last moment," it means "You lose hard because it's unwinnable". As I saw it, the Catalyst was offering a gun, and as others have mentioned, Shepard was awfully busy dying at the moment to really be in a good place to argue about whether or not it's the best solution they can put together. Shepard had two options: 1) fire the gun, destroy/control/synthesize the Reapers, and let galactic civilization pull itself back together from the ruins if it's capable of, or not if it's not, or 2) do not fire the gun, finish dying pointlessly right there on the Catalyst's nice, clean floor, and let everyone be wiped out by the Reapers.
 * If the controlling intelligence for the Reapers was always on the citadel, why did it need Sovereign and the Keepers to set off the invasion? Why not just set off the cycle itself?
 * Because the Reapers are an independent mechanism of the Catalyst. The catalyst set the cycle in motion and the Reapers carry it out, but it is willing to allow organics the chance to at least fight back, judging by its behavior. The fact that Shepard got that far and that it was perfectly willing to help Shepard make the decision at to what to do indicates as much
 * It explicitly states that it controls the Reapers. If it only started the cycle, as soon as they knew the Crucible was built and ready to kill/destroy/whatever them, they should have just blown it up, because then they win. Whether the reapers are independent or not makes no difference to the plot of ME 1. Sovereign was meant to send a signal to the keepers who then turn on the giant relay of the Citadel. If it was sentient, it could have done it itself when the time was up. So basically the existence of the Catalyst mostly renders the first game's plot a waste of time.
 * Because Protheans, that's why. The Protheans sabotaged the signal preventing the Keepers from activating the Citadel Relay. This was the last act of their dying race, after the Reapers had left the system. Now bear in mind the timeline here: for this to have been their final act, it would have to have come after their attempt at building the Crucible. Now, the Prothean VI on Thessia seemed to know an awful lot about the Catalyst, enough to explicitly state that the Protheans were well aware of how important the Citadel was to the Reapers. When the last Protheans made their kamikaze jump through the Conduit, they would have done so armed with the knowledge that the calls are coming from inside the house, so to speak, and would have engineered their solution to the extinction cycle accordingly.
 * What does merging organics and synthetics into "a new DNA" even mean? An established part of the setting is that different races use different amino acids so there's no way they all have similar DNA, and synthetics are said to be hostile to organics because they think differently, not their physical state.
 * Merging synthetic and organic would create an entirely new lifeform, with entirely new thought processes and bio-synthetic makeup.
 * That doesn't mean anything. It's Art Major Biology, which the rest of the trilogy avoids.
 * Check Joker's appearance. Notice any similarities to a certain Cerberus leader? Odds are, he meant merging organic life with Reaper bio-metal, which is an explicit ability of the Reapers. It's how they make more Reapers, after all.
 * He looks normal in my playthrough while running from the green if that's what you mean. It cut to black when the door opens so no idea if that's accurate.
 * Watched on youtube(got the destruction ending in my playthrough) and he looks normal after the door opens except his eyes are faintly glowing green and he has a geth-like code shimmering over his body like Shepard in project overlord.
 * Probably something like nanomachines were used to make the change. When most if not all species in the galaxy that are or were part of the community likely have omni tools, it's not hard to figure out the how. Medigel/Omnigel would probably be best to facilitate the change, not that that makes the whole thing better of course, just makes a little more sense. Considering that there's a lot of life without such things, even that sense is lost.
 * Shepard just blew up every single last relay in existence. Not only does this strand everyone on specific worlds, with their brightest and best stuck on earth, and caused the collapse of all galactic civilisation, but hasn't he just done the Reapers' job for them? We know blowing up a relay will destroy the solar system it is in, so every single one of those relays detonating has just wiped out countless trillions of organics in moments. Has the conclusion of Mass Effect 3 just railroaded the player into becoming the single biggest mass murderer in the history of Mass Effect?
 * There's no evidence that destroying the relays via the Crucible and Catalyst would trigger supernovas. We can presume that the Catalyst, being the one who built the relays, is smart enough that it could devise a means by which to destroy a relay without triggering unnecessary destruction. Its purpose is to preserve, after all, in its own twisted way. You can step down a nuclear reactor without causing a meltdown, after all, and the Crucible/Catalyst action was very much a controlled act of destruction. It is quite clear that the Catalyst prepared for this eventuality, so any destruction of the mass relays was factored into its plans, and none of those plans call for the mass destruction of hundreds or thousands of populated star systems.
 * There's no evidence that it wouldn't either, indeed given the Catalyst's motivations it would be surprising if it didn't cause the destruction of all the systems with a mass relay in it. The most of galactic civilization lives in the same system of an active relay, blowing up the relays at once will effectively do the same thing as the reapers, except not quite as thorough, organic life will still live on in systems without relays, but it would take a very long time for it to recover. As you can see it would be a very effective last ditch plan for the catalyst.
 * The Catalyst's motivations is to preserve organic life before their creations destroy them. Its solution was twisted, sure, but it "preserved" organics "in reaper form". Now, if you watch a recording of the endings, you will see that the glow in the gyroscope completely dissipates when it shoots an energy pulse at the next mass relay. In the red and green endings, the relay then lets out the energy pulse and a small explosion. In the blue ending, it doesn't even explode, just breaks up. When you watch Arrival, you will notice that the glow in the gyroscopes becomes bigger and then explodes in a positively massive explosion that completely whites out the screen. The little bursts you see in the galaxy map are only the energy bursts, not the explosions.
 * Bio Ware didn't help themselves by depicting the relay network's destruction as a series of massive explosions all over the galaxy map.
 * This troper figured they were depicting the radiation being dispersed to synthesize/control reapers/destroy sythetics, and not supernovas.
 * It's also bothering that, even if destroying the relays doesn't cause supernovas, Shepard doesn't know that. He knows exactly, what the hologram tells him and it doesn't say anything that may suggest, that the relays will blow in different manner this time. When the kid tells him that firing the crucible will destroy the relays, instead of saying: "What!? Won't that cause an armageddon?", he / she goes like: "Uh, ok, nevermind.". It is especially jarring after reading the codex - it says that the council races considered the destruction of relays in order to stop the reapers, but they concluded that there would be too many casualties and the cost is too high.
 * How/when/why was the Normandy making a jump when the citadel went all glowing-boom on everyone? The Normandy was on Earth at least in time to pick up Shepard's squadmates who got left behind in the charge. Shepard was known to be alive right up until the blast. Why are they abandoning the commander and trying to outrun the glowing light?
 * What's more, why are they trying to "outrun" something at FTL speeds and Joker just looks over his shoulder while doing so, as if it was just some car chace where that would actually let him see what he's running from? Also, are we to assume that joker was in the middle of a relay jump when that happened? That's an extremely small timeframe and a major coincidence. And if that was just traditional FTL and not a relay jump then why did the explosion affect the Normandy at all? Did the crucible affect ALL ships in the galaxy like that? So all the fleets got wrecked when it fired?
 * There were no "massive explosions" around the galaxy. Those are quite obviously the spread of the energy to do whatever Shepard decides to do. The only destruction that happens in the process is the collapse of the Mass Relays. And what is Joker trying to outrun? Again obvious: the collapse of the Relay Network. The Normandy is inside the negative mass tunnel when it begins to collapse, and it is this that Joker is trying to avoid.
 * In the "destroy" ending we do actually see a massive blast wave coming from the relay as it collapses after firing.
 * As to the question of why it affected the Normandy the way it did, remember that the Normandy was reconstructed with Reaper tech after the Collector Ship destroyed it. Presumably, every ship with Reaper hardware faced similar problems, but not every ship in all the fleets in the galaxy.
 * The Catalyst says that if Shepard chooses to control the Reapers, he / she will die. So... if Shepard is dead, how can he / she control them? Will they summon Shepard's ghost, or what?
 * Mind uploading. The body is dead, but Shepard's mind controls the Reapers.
 * Doesn't that ending contradict itself though? The Citadel isn't destroyed in that ending, and it seems that Shepard now has control over it, as it closes by itself when the reapers leave. Can't really point to the Crucible because nobody knew what it was going to do, just that it was going to be big and/or powerful. Anyway, if the Citadel is now under 'Controller Shepard's' control, then that means that the Catalyst was in control of the citadel the whole time, disregarding the whole 'the Crucible changed me' bit, even moreso negating ME 1 like mentioned above.
 * As far as I understand, Normandy was hit by a shockwave from an exploding relay. So, assuming that at the moment of explosion Normandy was at Earth (because why would they be anywhere else?): to escape from the shockwave, they activated their FTL drive. Before the hit, they managed to reach another star system (the planet they crashed on is clearly not from ours). The closest star system to Sun is 4 light years away. This means, that the shockwave from the exploding relay managed to cripple heavy armored frigate after travelling at least 4 light years. So how powerful was this blast when it reached Earth? Did anyone on the surface of the planet survived? Did Shepard accidentaly kill all the remaining humans on Earth?
 * You can see human Marines fighting on the surface and surviving when the blast sweeps over them. Mreach you own conclusion.
 * Well, we see what happens on Earth when the energy burst passes by, and the humans are untouched and in fact stand up to cheer. The Normandy appears to be travelling in a Mass Relay corridor (not standard FTL), and since the relays were in the process of being destroyed, the corridors were collapsing as well, and it is the destruction of negative mass space while traveling FTL that damaged the Normandy.
 * One important thing to note is that Mass Relay travel is instantaneous. There are no " mass relay corridors" for the Normandy to be traveling through. It's just travelling at typical FTL speeds, for some reason.
 * You're half right, from the Codex: "...[Mass Relays] can create corridors of virtually mass-free space allowing instantaneous transit...". You are correct in that transit ought to be instant but wrong in that there are "mass relay corridors". The blast wave appears to propagate around in a cylinder around the Normandy, however, as you can see a circle of black space behind the corridor. Perhaps this is yet another case of the Codex being an Unreliable Narrator, or maybe it's a "who knows what affect the crucible/energy wave has on the mass relays".
 * More-over, the scene takes place directly after the blast from the crucible is directed at the mass relay, after the initial explosion has dissipated. Assuming they wanted to give the impression that Normandy wasn't in a relay jump, they did a poor job of it simply through the timing of that shot. Also, why the hell was Joker looking over his shoulder like there was a damn rear-view window?
 * Because all the piloting skills in the world don't tell you what to do when you're being chased by a collapsing wormhole. He's running for his life - I'd look over my shoulder in a ship too, because there was nowhere in my training manual that told me what to do in case the Mass Relays begin collapsing en masse while I'm in mid-transit.
 * First, the Crucible fires some red / blue / green sphere. We see, that it doesn't hurt humans on Earth. After that, it fires another beam, that destroys the relays. I assumed that the Normandy was damaged by the relay explosion. We don't see how it affects Earth. Perhaps it's true that Normandy was in the middle of the relay jump at the moment, but seriously, what the hell were they doing out there? They were on the most important mission in history. They knew that Shepard is still alive (Hackett evidently knew it). 10 minutes earlier EDI saved the day, by helping Shepard to aim the missiles. It was entirely possible that they would need her help again. So what, did they suddenly decide: "Screw Shepard and this war, we are going on vacation"?
 * Shepard was still in communication with Hackett in the Citadel: Hackett may have heard the final conversation with the catalyst and realizing that the war is over but the Mass Relays are minutes away to be blown up, ordered the Normandy to lead the combined fleets away from Earth in order to diminish the number of troops stranded on a ruined world where feeding them would be problematic.
 * This is mostly a nagging curiosity, but what exactly constitutes a synthetic as far as the Crucible's red wave is concerned? Were Vigil, Mouse's VI Shepard, the Hammerhead VI, Avina, etc, destroyed? If not, would the Geth have been spared if they hadn't had Reaper code uploaded? After all, they were designed as V Is that could share experience, and it was only in this sharing that they became A Is.
 * Seriously, WHAT WAS WITH THE SHOCKWAVE? I see multiple discussions of it, here, and no one seems entirely sure what it was. Was it from the relay blowing up? Then why didn't it hurt the soldiers on Earth? Was it the "shut down/destroy all synthetic life" wave? Then why did it show up in the Paragon ending? And even in the Renegade ending, why would Joker know to run from it? And why would it destroy the Normandy, rather than just making EDI go offline? And...argh! I can grudgingly forgive the lack of a decent choice, I can accept that Shepard might have been too close to death to debate philosophy with the Catalyst, but the shockwave makes no sense and it's driving me crazy!
 * The shockwave is the spread of the energy of the Crucible that spreads throughout the Mass Relay Network. The Normandy is right in the middle of a jump through the Mass Relays when the network begins to collapse, and this destruction is what Joker is trying to escape. How are people still missing the simple and the obvious?
 * The problem is that it simply isn't that obvious, hence all the questions about it. You could ask 10 different players and get 10 different opinions on what happened.
 * Hell, even if it was more obvious...why the hell is Joker taking the Normandy through a relay? As I said above, he had no way of knowing what it would do to EDI, and even if he did, would he really run away without knowing whether or not Shepard was okay? Hell, would EDI let him? Again: no friggin' sense.
 * Bioware have a track record of being great writers making great games. With that said it boggles the mind that the writing or gameplay in the ending wouldn't make fans happy. The theory of it all being a ploy to sell DLC makes this even worse, as if this is a deliberate move then a lot of fans will feel betrayed.
 * The after-credits scene implies that Shepard's story has become a legend passed down through many generations, and that the entire series was being told by an old man to his grandson. If this is the case, then how could the scene in the Citadel be part of the legend, if Shepard doesn't survive to tell about it?
 * There's no actual indication that the old man knew the exact details about what happened. More likely, they pieced together the truth after a long period of analyzing the wreckage. Hell, the old man could have made up some of that entire scene.
 * The most egregrious part of the old man scene is that it happens in ALL endings no matter what you choose. Kind of makes the whole point moot if all but the bad endings lead to the same conclusion.
 * If the entire series was an old man's bedtime story, it does make the sex scenes that much more hilarious.
 * There's no indication that the whole series was just his story (his 100+ hour story featuring regular "planet scanning" scenes). It could just as easily be argued that what you see is what really happened and the final scene is just showing that Shepard is still remembered long into the future.
 * So the Catalyst says that if all life is turned into organic-synthetic hybrids then the universe will be saved. For sake of argument, I'll take him at his word that this will avert a organic/synthetic war. However, for the Destroy option he clearly states that people would inevitably create more synthetics in the future... what exactly stops them from doing that in the Synthesis ending? The technology for creating synthetics is still going to be around, and people are going to want to keep making them for all of the same reasons, in addition to researching the biological and technological miracle that just affected the entire universe. My point is, what's to stop a organic-synthetic/synthetic war in the Synthesis ending? Did that green energy wave rewrite everything to the point where all synthetic production now produces organic-synthetics? But the parts you would use to build a synthetic are just parts, they're not "alive" until you put them together... or are all the metals and microchips organic-synthetic too?
 * Did EDI spontaneously grow a vagina in the Synthesis ending? It's a valid question.
 * Are you asking if EDI became part organic along with all the organics become part machine? Interesting question, but we only see them on the crash-landed planet briefly so we aren't given time to dwell on it.
 * Not quite. It's stated that all synthetic beings will become part-organic as part of the Synthesis ending. But if all organics and synthetics become the same universally compatible "race", does that mean that EDI suddenly grows reproductive organs that were not part of her original design? If not, then doesn't it undermine the concept of Synthesis as a method of eliminating discrimination between synthetics and organics?

Last Ten Minutes

 * So named to avoid accidental spoilers, since this folder should be titled "The Catalyst," mainly because this thing is one huge head scratcher by itself. We won't go into the Ass Pull vibe this entire ending gives off since that's subjective, so lets just simplify this to its most basic elements.
 * First, where did this thing come from? Mass Effect is known for having a game changing plot twist about halfway through the game, but this guy shows up right at the end, and we're just expected to accept it. When they revealed the Reapers in ME 1, we could go along with that because these guys were Robot Space Old Ones right out of Lovecraft, and when you replayed the game it actually subtly built up to that unveiling in a way you only notice the second time around. In ME 2 the Collectors being genetically modified Protheans also made since because it was a possibly Red Herring for what galactic civilizations fate at the hands of the Reapers might be, and it solved the problem of the Collectors being this new race that was never spoken of before; because they were spoken of before, we just didn't know they and the Protheans weren't one in the same. The Catalyst? Literally comes out of no where with no build up or explanation. Some might argue that's the point of a plot twist, but to paraphrase a certain internet reviewer: "Yeah but that's like saying Mrs. Brisby was broccoli the whole time. Yeah you didn't see it coming, that doesn't mean it makes sense."
 * What Mass Effect games have you been playing? Mass Effect games have always had a big reveal right at the end. Remember the Citadel being the trap? Remember the Human Reaper? And while the exact form of the Catalyst was not foreshadowed, its existence was stated right at the beginning of the game when Liara explained the Crucible, and the Catalyst being the Citadel was brought up when you attacked the Cerberus base before the climax. The Prothean VI on the Cerberus base even confirms that the Reapers were part of a larger plan by something else that instigated the cycles all along, which was also hinted at by Javik. So nope, this assertion that either the Catalyst breaking from the previous pattern of ME games or that the Catalyst was not foreshadowed is flat-out wrong.
 * The closest thing to foreshadowing would be the established fact that the Citadel and the Reapers were connected; previously established as "Reapers built the Citadel". It isn't that surprising that the citadel had some other purpose in the reaper's plan beyond a model to guide galactic technological development.
 * Actually the other purpose was already established since ME 1: "The Citadel is in reality a gigantic Mass Relay that summons the reapers back to galaxy".
 * It was vaguely alluded to when the Reaper you take down on Rannoch tells you that the Reapers aren't the ones who created the cycle.
 * Two, who the hell made this thing? The civilization of the first cycle? Apparently this thing wants to end war between organics and synthetics, but isn't he synthetic himself? Is he the natural evolution of the first cycles version of the Geth? This is different from the first point because it is clear something had to create this computer program, but who did it and to what end? Is this just an example of the worst kind of AI Is a Crapshoot mixed with the most ridiculous Freudian Excuse ever? And a side point of this: who the hell made the Reapers? This thing doesn't have fingers, so what did it possess some ship abandoned ship making factory without anyone noticing, tricked the first organic civilization into melting themselves down and letting that power the first Reaper? This thing said it created the Reapers, well I'd like to know bloody HOW he managed to do that!
 * Considering how many tens of millions of years ago this took place, it's possible he was a creation of the first civilization to reach the galactic level and proceeded to slaughter the organics that made him. His actions are possibly driven out of guilt from having done this. First reapers could have been made out of their corpses when the dust settled. This is all wild mass guessing, of course. It's also likely that the first few cycles, hell, first few dozen cycles were an ironing out the kink's process until the established system fell into place as the most efficient. Which makes you wonder what else it tried.
 * Three, his motivation makes no sense. We're lead to believe every cycle has had its version of the Geth being created and inevitably realizing they are superior to their creators, or something along the lines of what happened to the Quarians happens and they attack, whatever the case: war breaks out. Lets put aside the fact that this thing is, by definition, a synthetic itself, so is it just a maverick defector from decadence who wants to save organic life from his own kin? I might buy that, sure, but it still doesn't make any sense. Lets say the first time this happened in the first cycle he considers it a fluke, and just puts his Reapers on reserve juuuuust in case. Once bitten, twice shy, I'll give him that. Then it happens again and well now he's justified, in his mindset, to enact his plan of preserving organic life once more. Then we're lead to believe this exact case of organic civilization threatening war with synthetics happened OVER SEVEN HUNDRED TIMES!? And THIS was the one time it didn't go the way it always had? THAT is a statistical IMPOSSIBILITY! Writers Cannot Do Math on an unforgivable scale!
 * It appears that the 50,000 year cycle is intended to "nip the problem in the bud", to prevent an advanced civilization from producing synthetics that would then rise up against their creators. That didn't work for this cycle because the Protheans blocked the control signal to the Keepers centuries ago--Sovereign's previous attempt at bypassing the keepers was the Rachni wars in 300 CE, well before the Geth Morning War in 1895 CE. Thus, without the scheduled culling, synthetics like the Geth and EDI/The Luna AI were allowed to rise. My guess is that the catalyst/reapers make the assumption that all created will rise against their creators and produced the solution without testing their assumption against other synthetics, and so made a wrong assumption that resulted in millions of years of galactic genocide to prevent synthetics from even being created in the first place.
 * From what we know it's apparent that the cycles don't always go off cleanly; the protheans apparently dealt with the A.I. problem fairly early on in their cycle, as well as the protheans managing to throw quite a few wrenches in the reaper's gears.
 * Conflict between synthetics and organics stretches back to the first game. The "signal tracking" mission AI says that organics always have to enslave or destroy synthetics, Tali says organics can't negotiate with synthetics because there's nothing organics have that they want. The second game establishes this paranoia deeply in overlord and the EDI mission, and Javik says about the same thing in the third game. That Shepard has temporarily managed to negotiate a treaty between geth and quarians (and that's a pretty tall order in itself) very well may be the first time it's been done in the game universe's history, and demonstrating that you've been able to temporarily stop a 300 year war before Admiral Xen starts randomly dissecting geth again isn't the strongest counterargument to the catalyst's experience.
 * It should be enough that any reasonable being should pause and say "Let's see how this goes. I'll give you another century, and if the Geth and Quarians are still working together we can talk about ending the cycles."
 * What's most appalling about the motivation is that there's an obvious one that makes far more sense presented through the game. If the Reapers hadn't wiped out the Protheans, humanity (and all of the other advanced races) would have either been enslaved or obliterated by the Protheans. This makes far more sense as the purpose of the Reapers as 'salvation' through destruction: the Reapers exist to allow for new sentient life to flourish, while saving previous civilizations for posterity. This also makes the decision to stop the Reapers a bit more grey: destroying them saves humanity and the other current races, but essentially destroys or limits the possibilities for any future races (e.g. yagh).
 * Whoa, that just blew my mind. That would have been totally logical and fit with the previous games' established themes/continuity too. Also see Aborted Arc in the main entry for the original motivation that Bioware came up with in game 2 but abandoned.
 * Four, where did the 700+ synthetic races go? It melts organic life down into Reaper goo to preserve them because synthetic life is inevitably going to win, or something, ok. So where the hell did the synthetic life go? They didn't melt the Prothean's version of Geth down into Reaper goo, so where did they all go? Did they just genocide the synthetic life as soon as they made the new Reaper and go back to sleep waiting for the next 100% assured organic v.s. synthetic life war to break out? Doesn't that make this thing a hypocrite? Not saying we wont buy the genocidal villain being a hypocrite, but it still seems rather... logicless? Anti-logic?.... Stupid, that's the word I'm looking for.
 * "No. We harvest advanced civilizations." They don't kill all organics, they harvest all advanced civilizations, which would imply the synthetics are destroyed as well.
 * No, they don't. They say they harvest every advanced civilization and "save them", but that is contradicted by the fact that they only harvest humans. Why not "save" the other species? All the talk about genetic diversity and other being genetically inferior or something shouldn't matter if the Reapers cared about saving them. The asari, turians and salarians (maybe the quarians too) are still more advanced than the humans.
 * No, they're harvesting everyone. Species deemed "worthy" get turned into Reaper capital ships, while "lesser" species get turned into destroyers. Humans were going to be turned into capital ships, while the other species were going to be turned into destroyers.
 * It's implied pretty clearly in Mass Effect 2 that the Protheans were not worthy of being made into a Reaper at all, generally pointing to no species in that period becoming a reaper. (Humans being genetically diverse and varied enough that they made good 'material'.) Rather the Protheans being repurposed into the Collectors being the 'ideal' solution. Even if nothing is said of the other 'Prothean' species, the implication still stands, that the Reapers simply culled that whole civilization, sans Collectors. (Can't forget that another writer was brought in late in the game, which explains such incongruities.)
 * Then they are not saving the other species, as they give them weaker armor. Would make more sense to harvest many destroyed and use normal machines as destroyers. Basically, they use lesser species as fodder that, while hard to beat, it much easier than a Capital ship to beat. Shepard downed one with a single Cain shot.
 * No, s/he didn't. S/he took down a Reaper anti-"air" cannon with a Cain, which is visually distinct from a Destroyer. There is no evidence that Destroyer have weaker armor than Capital-class Reaper, and seeing how it took the mother of all Thresher Maws/ the entire Migrant Fleet/ several Thanix missiles aiming squarely for their weak point to destroy one, uh, Destroyer, it's rather unlikely that their armor is that much weaker.
 * Five, at what point do they consider organic life a lost cause and start the harvesting process? Because if we are supposed to believe this is all to preserve organic life because they'll lose against their own synthetic creation, then when do they start the invasion? This is asked because for this current cycle, that war is with the Geth. So, was it as soon as the Geth were made they started their plans for genocidal reproduction? (heh, Reaperoduction) or did they wait till the war with the Geth vs the Quarians to break out, or wait for the Quarians to get kicked off their home planet? Well, we know for a fact they didn't wait until the Geth actually started a war against all organic life to emerge the superior life forms, because the Geth DIDN'T START A WAR AND JUST STAYED IN GETH SPACE AND LEFT EVERYONE ALONE! The ONLY antagonist Geth in the series were controlled by the Reapers! Oh hello there, giant contradiction: the Reapers invade because synthetic life threatens organic life, and yet the only reason the Geth threatened organics was because the Reapers were starting their invasion. Whaaaaa?
 * As noted above, the scheduled culling was well before the Geth came into existence (Due to the Rachni wars being the first occurrence of Reaper involvement in this civilization cycle), so the decision on when to attack isn't based on the state of the galaxy, just when the timer goes off. It didn't work this cycle because the car keys didn't work when Sovereign decided to go pick up his friends in response to the alarm clock.
 * Six, Wrong, wrong, wrong! The Catalyst is WRONG. Synthetic life WASN'T threatening Organic life, at least not during this cycle, at least not yet. We saw evidence of that in, again, the friggen Geth minding their own damn business unless someone screwed with/indoctrinated them, and in EDI being pretty cool and nice and stuff to say the least. I'll forgive the fact they jumped the gun a little considering they're Well Intentioned Extremists to the max long since gone off the Moral Event Horizon, but the fact you can't use this argument against it at the end is just dumb. You can't use LOGIC and RATIONAL and PHYSICAL EVIDENCE against an emotionless machine? Really? You have no choice but to go along with the DeusExMachinas BS brigade and presented with the Endingtron 9000 to make a completely binary choice to decide the ending of the game that completely rips off Deus Ex Human Revolution and yet somehow manages to be even more disappointing? How the endings are pretty weak for various reasons is better detailed in the folder above this one, but EVEN if you wanna argue that was the point, that the writers wanted this jerk to come off as hopelessly and pointlessly wrong and so stuck in its own ways it has completely ignored the fact his own stated motivations don't apply anymore, the fact they expect you to just go along with it instead of being allowed to call him on it is just awful, and makes it come across from a narrative standpoint as if we are meant to take everything he says at face value.
 * This one is made worse by the Illusive Man, especially as a full Paragon. Shepard just talked a completely indoctrinated maniac into accepting that his entire reasons for everything he has done is wrong and convinced him to kill himself to prevent causing further damage. AGAIN. Then a few minutes later he doesn't even make the attempt to reason with the being of pure logic, he just takes what it says on faith.
 * Well, there is some justification for this. The reason Sheppard can't really argue with the Catalyst is because at the end of the day the Crucible still has to be fired, which will invariably destroy the mass relay network. The Catalyst itself has no direct power over the Reapers, as they are it's autonomous creations, so even if Sheppard managed to convince it that it's logic is flawed he would still have to choose in what way to fire the Crucible. Also, the Catalyst already realized that it's logic no longer applies when the first organic ever reached it, marking an unprecedented occurance in the Cycle. The Catalyst is not omnipotent and the crappy options that Sheppard is presented with are the only ones that were within the Catalyst's immediate capabilities to offer. Why the writers thought that setting up a situation like this is a good idea, on the other hand, is a different matter entirely...
 * Not sure where the idea that he created the reapers and they are autonomous comes from, the only explanation he gives for his identity is "I control the Reapers."
 * It says it created the cycle so, by extension, we can assume that it created the agents that perpetuate the cycle.
 * It still stands that he flat out states that he controls the Reapers, so he should be able to just stop them, or blow them up, or make them kill each other. He probably does give them the ability to work by themselves, while the final decision on things is up to him. No real explanation is given to why he is being such a Jerkass. It also still stands that if the citadel is sentient, why he didn't just do Sovereign's job for him.
 * Another possibility about the Catalyst, and by extension, the Reapers: they may be like Saberhagen's Berserkers: that is: they were created by someone who had a goal which made sense, but after so many eons of activity, they core programming, their raison d'être, degraded and they developed a new twisted goal which was a travesty of the original. For instance, maybe the original goal of the Catalyst was to use Reaper capital ships as arks to take in refugees from organics civilizations being destroyed by their synthetic creations, where outfitted with heavy armors and death ray to be able to survive a violent encounter with genocidal synthetics, and used indoctrination only to convince frightened organics that the big mecha-cthulhu ships where in fact friendly. But after untold millions of years, the programming of the Reapers got corrupted, and they decided that conserving intelligent species DNA in a paste and their culture as data stored in a Reaper memory bank was a satisfactory way to "preserve" them, hence the implementation of the genocidal cycle.
 * This looks more like it belongs in WMG, not Headscratchers.
 * If there was an entity that controlled the reapers and was aware of the outside world, then how was the cycle delayed? Wouldn't it be aware to that something had gone wrong and do the things Sovereign couldn't do in Mass Effect 1? And by extension, if the Catalyst controlled the Reapers then what was the need for them to be sentient and autonomous?
 * Fail safe so that if the citadel was ever tampered with (which it was) they'd carry out the cycles anyway.

Flash Back Spoilers:

 * Here's something that doesn't make sense to me regarding the flash back, no matter what, you have to get one of the ME 1 love interests, and it defaults to Liara if you have romanced anyone else/not romanced anyone... what I don't get is, why isn't Garrus shown? He's been with Sheppard the whole way like Joker, and it's pretty easily established that Garrus is Sheppards best friend by this game, look at their banter, the random conversations, hell, their final conversation cements it, promising to meet at heavens bar. I won't get into why the other love interests aren't in his head at Shep's final moments, because while that makes me angry, it doesn't make me as mad as leaving out the proven best friend thing with Garrus, unlike Liara, who's merely on good terms with Sheppard.
 * Because Liara is the Creators Pet. Simple as that. Excepting the VS, no one gets a flashback besides her. Also notice how she gets along just fine even on a quickstart (whereas everyone else in the galaxy gets screwed) because she didn't even need Shepard to help her with the Shadow Broker.
 * Not quite. All the ME 1 love interests do. Getting "flashbacks" for anyone else was deemed "too expensive," so there's only Joker, Anderson, and whoever from ME 1 you're closest to.
 * Seriously? Sepia-toning 10 more still images would be too expensive? It would take me a day to set up, capture, and sepia tone 10 images of premade models, and I'm not even an artist!
 * Hell, it's a basic tool on ANY video editing software. Including the free ones. Was a stern look or a smile too much to put a filter over and send it in?
 * But guys, Bio Ware needs the money and this can only be done with DLC. Perhaps 800 MS points for an additional 5 sepia-toned stills and one additional outfit for Conrad Verner. YMMV. On the serious side, the creators must have thought the beach scene was good enough and that no further consideration need be given to any other characters.
 * Actually, the flashbacks were remarkably well-animated. The facial expressions looked smooth and realistic. We all know Bio Ware is terrible with facial animations. That said, I would have accepted regular facial animations, and not necessarily the smooth and pretty ones that Joker, Anderson, and the ME 1 LI got.
 * Liara, Joker, Anderson, and the VS are the only major characters from all 3 games that are guaranteed to be alive at the finale. Garrus, Tali, Wrex, etc can all die at various points, so many they just limited it to the first four for ease of video editing.
 * Wrong. The VS can die at The citadel if you can't convince them that Udina has turned traitor.

Collectors in Reaper forces
Now this is admittedly a very minor quibble, but I might as well ask. I was looking through the Codex (specifically, the "Miracle at Palaven" entry for the Reaper War section) when I found this sentence. "The Reapers did not understand the seriousness of the threat at first--those that detected the landing crafts sent husks and Collector swarms to intercept them, but little more." If the Reapers still have the Collectors and/or their resources at their disposal, then how come Shepard never comes across them? Or any NP Cs, for that matter. Yes, I am aware that the Reapers use those Oculus things as fighters, but I don't think that's what they were talking about.
 * It's a big war. It stands to reason that Shepard simply never found them. They canonically still are in the Reaper forces, so we'll probably get a DLC with them.
 * You wiped out the vast majority of them at the Collector Base. They are probably being concentrated in areas where they might be the most use, and as Shepard demonstrated, that's not against him/her.
 * "Collector swarms" refers to the artificial insect things that the Collectors used to paralyze people in colonies for abduction. Even if the Collectors are all gone, it makes sense for the Reapers to still have the template for the swarms ready at hand, and they make a very useful tool for breaking resistance.
 * Those are "Seeker Swarms", not Collector swarms. This troper figured the Turians killed all of the Collectors with their badassery while defending Palaven.

Discrepancies in Prothean physiology (Major spoilers)
Mass Effect 1 established a rather surreal image of the Protheans on Ilos by showing statues of them as spindly, long-limbed humanoids with tentacle faces. Mass Effect 2 continued this in their codex entry with a husk-like, but otherwise identical, Prothean. The Collectors. Mass Effect 3's codex page retains the husk-prothean image, but. In short,
 * First of all, there's no real evidence that the tentacle-faced statues were supposed to be Protheans of Javik's species. They could have been anything. They could have even been one of the "lesser" species incorporated into the empire. Second, the Collectors only resemble the Protheans in the most extremely superficial ways. Going by Javik's appearance, the original Protheans did not have chitnous skin, glowing eyes, no mouths, armor plating and insect wings. If a human were covered din armor, grew insect wings, had glowing eyes and no mouths, that would be an example of "drastic mutation".
 * This is supported by statements made by Javik that the ruins of Ilos are not Prothean at all. He mentions that the ruins on Ilos were from a previous civilization, the Inusannon, and that the Protheans built on top of the ruins of that previous civilization.
 * I think the tentacle aliens were maybe the leaders of the Prothean empire, and the Javikans (it's as good a name as any) were the soldiers. It would therefore be natural for the Reapers to use them as the template for the collectors, as they are more physically powerful. And/Or all the tentacle aliens were used to make a Reaper.
 * Javik does mention the Protheans building on the ruins of older races. It's possible that the statues belonged to an earlier cycle, and historians just got it wrong.
 * In one of his conversations Javik outright states that the Protheans built over the previous civilization on Illos.
 * Though he also makes clear, in the very same conversation, that "Prothean" referred to numerous species, rather than one.
 * That doesn't reconcile the fact that the creatures in the Beacon visions that were slaughtered by the Reapers and turned into Collectors were the tentacle-bearded humanoids, though.
 * What makes it even more confusing is the art books depict protheans with tentacle faces also.
 * The new Protean appearance is a retcon, based on the appearance of the Collectors who most likely became repurposed Protheans only after their appearance had been set in stone. The tentacle-face was scrapped because it would have required completely new motion-capture work and animation to get the strange physique to work correctly; having those long, pseudo-tentacular limbs climbing ladder for example would have required more work than the character was worth.
 * Word of God states that the tentacle-protheans were actually Javik's race's predecessors; they were essentially the "protheans" to the Protheans. (I can't find the link, not now)

Really, Virmire Survivor?!

 * You are seriously going to side with the unrepentant asshole whose done nothing but hinder you and has just openly admitted to aiding the enemy over your own commander, best friend and (possibly) lover? Look, I can understand the emphasis on the Sadistic Choice, but this particular instance just feels like a last minute addition at the expense of the Survivor's character. Yes, you can convince them to stand down and help you take down Udina, but you shouldn't even have to covince them after all they've been through with you.
 * To be fair to the Virmire survivor, he/she genuinely doesn't know whether or not you're under the control of Cerberus. For all he/she knows Shepard was just trying to regain his trust to throw him off. Udina's a dick, for sure, but nobody ever really thought he was working for Cerberus. Remember, as Miranda noted, it was as simple as putting a chip in your head during Project Lazarus to put you under their complete control. That's what the Renegade and Paragon dialogue choices reflect. If you're far enough on either side you're able to convince the VS to give you the benefit of the doubt and question Udina. If you aren't, then the VS instead takes Udina's word over yours.
 * Shepard really shouldn't have come through that door with weapons raised in the middle of a terrorist attack by the people s/he was just working with a few months ago, while there's still some doubts being harbored in Ashley/Kaidan's mind. Shepard happening to show up in the middle of the Cerberus attack while an assassin is chasing the Council is really going to set off at least a few suspicion bells in the newly-appointed Spectre's head.
 * Wait, what? Shepard shouldn't have his weapon drawn in the middle of a terrorist attack? That's just stupid! Sheppard SHOULD have his/her weapon out, Kai Leng or any other Cerberus force could of been waiting for them and the council on the other side of those doors, not to mention, Udina was there and Shepard needed to take him in/stop him from getting the rest of the Council Killed. Assuming other wise is just plain stupid. Kaidan/Ashley are being idiots, if it wasn't for the fact I thought I'd need Kaidan's powers back on the Normandy, I would of told him to piss off.
 * No, I didn't say that Shepard shouldn't have his/her weapon drawn, i said Shepard shouldn't have the weapon raised while bursting into the room that the Council was in. Charging into a room with a VIP and a twitchy bodyguard with weapon high and ready to engage, and then drawing down on one of the VIPs is going to automatically make Kaidan/Ashley wary. This coupled with the fact that they're still somewhat wary of Shepard and have not yet worked out that suspicion, on top of the fact that they don't know Udina is a traitor. How would you react if someone who formerly worked with a terrorist group - the same one attacking at that moment - rushed into the room where you were guarding a group of VIPs with a weapon drawn and leveled at one of those very people? The fact that Ashley/Kaidan didn't shoot Shepard right off indicates rather remarkable discretion, restraint, and trust.
 * It becomes downright hilarious if you're wearing the Cerberus Armor Set at the time.
 * The Virmire Survivor is not required to take a position just because Shepard wants them to. It doesn't matter whether or not Shepard trusted Udina. What matters is that the VS was a Spectre, there to protect the Council, which Udina was a member of. And it isn't like Shepard gave the VS any special reason to trust them fully beyond their own word. Coming in at that exact moment, guns drawn probably wouldn't end well if you wanted to seem trustworthy. They don't have the meta-knowledge you do or the in-game knowledge Shepard does.
 * To be fair to the Virmire survivor, their major worry isn't that Shepard is a traitor. That worry got put to rest in the Mars Archive. What they're afraid of now is that you're indoctrinated. After all, by this point you already know that Cerberus troops are at least part-husk... and the last person the Virmire Survivor saw with as many Reaper-tech cyborg parts jammed into their body as you've had jammed into yours? Saren.
 * One of the most common forms of Wrong Genre Savvy is believing that you're the hero. The VS just got promoted to Spectre status; from there perspective, they're the hero and Shepard is The Mentor or their Always Someone Better. If that were actually the case, then the Cereberus attack would be exactly where I'd expect the reveal that Shepard was secretly evil to take place.

Last Mission

 * Not an indicative folder title, but, y'know, spoilers - why are there so many old-style telephone boxes in Future!London? And how the smeg are they still standing after weeks of Reaper smashing?
 * Do I even need to make the joke?
 * Doctor Who uses a police box, not a phone box. Could just be something they kept and just updated them with future tech? Just kept the look of them for aesthetics? (Granted, to me they look terrible.) Unless you can look inside one, (which I couldn't) you don't know.... Other then that, your fighting the penultimate battle for earth, and your concern is how a phone booth in the future looks?
 * Maybe there was a retro-fashion fad going on. And they're not necessarily just phone boxes, but could be public information booths, bit like the Avinas on the Citadel.

Submachine Guns

 * So, we all know the M-25 Hornet has terrible muzzle climb. I wonder if it might have anything to do with the fact that Commander Shepard, along with everyone else in the galaxy, is holding the gun the wrong way. That is clearly a foregrip just under the muzzle, but characters always wield it with both hands on the aft grip, like they would a regular handgun. The M-12 Locust and the N7 Hurricane also have this problem, though thankfully lack the accuracy issues. Makes you wonder why they designed them that way if no one ever wields them properly...
 * That's also a bit of contention for this troper, as well. While it's understandable that the player holds the M-4 Shuriken that way, seeing as it's a machine pistol as opposed to a full-on SMG, the Tempest, Locust, and Hurricane are all proper SM Gs...
 * It's more of a development issue. Instead of creating separate poses for each individual gun, it's a lot easier to create five-six different poses and call it a day (though I think that SMG and pistol share the same pose). This is more of a problem to Third Person Shooters as the character model is in full view (Gears of War avoids this problem as it has a much smaller weapon selection compared to the one Mass Effect provides). First Person Shooters have a less of a problem as the "arms" of your character can be part of the gun model instead of being a wholly separate model.
 * On a similar topic, why are SMG's still considered a separate weapon type at all? It was understandable in ME2 when not every class had access to Assault Rifles, but now with the weight system, that's not a factor anymore. There are only five SMG types in ME3, and they all seem like they could easily be relabeled as either rapid-fire pistols (like the Shuriken) or ultra-lightweight assault rifles (the Locust). It's baffling that they an entire weapon type that doesn't really do anything.
 * I believe it's more for 2 gameplay reasons: 1) power-heavy characters have the option to carry both a light 'SMG' and a pistol (SM Gs generally better against shields/barriers and pistols generally better against armor), and 2) all squadmates have access to 2 weapons, but a couple of them only get access to SM Gs and pistols to balance their strong powers (Liara and EDI, IIRC). Giving them assault rifles would overpower them (I presume).

Cerberus Attack on Sur'Kesh

 * Did anyone ever explain why the Illusive Man wanted Eve killed? Most of Cerberus' activities can be reasoned out, even if they're not explained explicitly, but what was up with the raid on Sur'Kesh? What benefit was there in stopping the genophage cure, or provoking a war between the krogan and salarians? Sure, those things probably wouldn't hurt TIM's plans, but how did they benefit them? And hell, if you wanted to assassinate a target, why wouldn't you send a few of your cyborg ninjas? You're telling me they crammed a frickin' ATLAS onto their ship, but couldn't fit a Phantom or two?
 * Rogue cell.
 * Cerberus is, technically, working on the same side as the Reapers. TIM is also indoctrinated. Remember that indoctrination is subtle, especially when the Reapers want to maintain your full functionality, and going by how the Reaper indoctrination worked firsthand on Grayson in Retribution, the Reapers can very easily turn your own emotions and motivations around to suit your plan. So, while TIM would not normally attack the Sur'kesh base, the Reapers may have altered his motivations, observations, and conclusions to reach a point where he would decide it was in his best interests to target Eve.
 * A cure for the genophage would certainly not go along with the ideals of a human supremacist group. Add a little indoctrination into the mix, and we have a TIM who really doesn't want to see the Krogan back in shape.
 * Hmm, good points. That actually might flip this over to Fridge Brilliance for me, since it hints from very early in the game that TIM's serving the Reapers' interests more than he is his own. Though the lack of Nemeses and Phantoms is still obvious Gameplay And Story Segregegation.
 * Just to add to your headscratcher, in ME2 TIM's report after Mordin's loyalty quest is that the cure would have been useful, and will berate you for destroying it or praise you for keeping it, as the krogan would make good shock troops against the Reapers. So when he was thinking clearly, he wouldn't have wanted to kill Eve. Heck, he would have funded your expedition to save her from the salarians. But he's not thinking clearly, as said above, he's indoctrinated.
 * It's mentioned continuously that the Krogan were a massive threat post-Rachni War, to the point that the genophage was considered a viable solution. It's also pointed out by at least two party members (Garrus and EDI) that the Krogan will see a massive population boom with the genophage cured, and other characters consider the cure a major long-term problem; it's just that short-term survival renders that argument moot. Given TIM's beliefs and goals, avoiding a second war threatening humanity after finishing off the Reapers by inserting a strike team to kill one lone Krogan is a pretty simple solution.

Ah, yes, "ducking"
When Kai Leng and Shepard have their stand-off at the Citadel, why doesn't the Salarian Councillor duck so you can get a clear shot at him? Instead Valern/Esheel just stands there and makes it impossible to attack Leng.
 * If Valern/Esheel ducked, it would break the standoff, and Leng would likely just shoot him/her then bolt.
 * It's like Zaeed said back in 2; "The only people who don't freeze up when they have a gun pointed in their face are trained killers and psychopaths." Apparently, the councillor is neither.
 * With the other nonhuman councilors being a turian - whose culture emphasizes a mandatory period of military service - and an asari who is several hundred years old, and whose culture doesn't make combat mandatory but was still encouraged to learn to fight as a maiden, the shorter-lived and more delicate salarian is the only one who could plausibly be unfamiliar with having short-range weapons pointed at their face.

The Citadel and Relay Network

 * What happened to everyone on the Citadel when it was taken by the Reapers? A lot of my favorite characters were on board! Aria, Bailey, Liara's dad, possibly Dr. Chakwas and Mordin, the Council (love to hate 'em), Kolyat, Kelly, Dr. Michel, all those other lovable background npcs...
 * I really wonder about this too, because you can see traffic still flying around on the wards, which makes me wonder if everyone in the wards is still there and going about their business as if nothing happened.
 * As Vigil explains in the first game, once the Reapers take control of the Citadel, they have total control over the Relay network. The Prothean Empire, and the civilisations of the previous cycles, were defeated -- in part -- because they could no longer make use of the Mass Relays around which their society was built. Reinforcements? Impossible. Communication? Impossible. So why on earth do the Reapers allow the use of the Relays once they've claimed the Citadel towards the end of the game?
 * Because the Catalyst wanted the fleet to reach Earth in the first place to challenge the Reapers.
 * I'd be more willing to go with a handwave that the Crucible itself had some sort of jamming signal to prevent the Citadel from being used to its full extent. The Catalyst, after all, tells us that it couldn't even conceive of "another solution" until the Crucible had docked, so the idea that it wanted the Reapers to be challenged seems implausible at best. Until it's altered by the Crucible, the Reapers were doing everything in their power to reap as they would normally reap. And, regardless, that there's no attempt to either explain or question why the Relay Network hasn't been shut down remains a pretty glaring omission. I honestly have to wonder if the writers simply forgot what the Citadel was capable of in Reaper hands.
 * We actually do get an explanation for why they can't control the network way back in the first game. They control it by controlling the Keepers, and the Keepers no longer respond to their commands. Sovereign had to physically interact with it to try and activate it's own relay, and they may well have simply not had time to get it up and running at full capability yet. Since we never find out how they took it, they might have just gotten an indoctrinated agent on the controls and flown it there under it's own power (it was established early on that the races living there have no idea what 90% of the stuff on it does), then the attack comes as soon as they get it parked.
 * That the Keepers no longer respond their signal is irrelevant if they have indoctrinated followers capable of activating the command console, as Saren attempted. They must have already have had a Reaper physically interact with the Citadel to fly the thing to Earth, after all. That being said, the entry on the Crucible's "Inferometric Array" mentions that the Crucible is, indeed, capable of tuning into the command switches of the mass relays....
 * So that sounds like they used the Crucible to turn on the mass relay back to Earth, which I suppose would explain why that's the only place you can go.
 * Allright, so at some point the reapers decide to get the citadel back, and do so with such an humiliating ease it apparently took them five minutes top (So no one on the citadel apparently could do the smart thing and close the arms, WTH?). No one ever wonder about what happened to the millions of people on the citadel (though dead or huskified are pretty safe bets).Then the Reapers...I don't know, tow, I guess, the whole whooping citadel through the nearby relay (damn those things are hardcore, that one just shallowed a space object a hundred time bigger than himself). Then they took it to Earth, probably because the plot say so. That whole sequence headscratch me so hard I probably just bore a hole in my skull.
 * First, why would it be a stretch for a Relay to move the Citadel? There's never been an established upper limit to what they can move. There's also no evidence that the Reapers took it over in "five minutes top." We just learn that while the Fifth Fleet is storming the Cerberus base that the Reapers took the Citadel and moved it. Third, there's no indication that the Reapers did anything to the people on the Citadel; from what we can see inside the Citadel's closed Ward arms, there's still plenty of orderly traffic moving around. Most likely what happened, judging by TIM's presence, is that Cerberus took control of the station's control systems and moved it per Reaper orders to Sol. Somehow.
 * It'd be a stretch because the Citadel is FAR larger than the meteor that Shepard destroyed the Alpha Relay with, which was way too big for the relay to throw/cast(judging by the fact that the Alpha Relay apparently tried to do so before it was destroyed).
 * No. Mass relays do not automatically attempt to send anything through them if they approach. Any object passing through the relay has to communicate to the mass relay first to tell it where it wants to be sent or even if it wants to be sent.
 * It's possible that the Citadel can move by itself, if directed by the Catalyst or the Reapers. It is the single largest concentration of Element Zero in existence, and the heart of the Relay Network after all. It could just use the Network as a guidance system, and make the jump under its own power.
 * For that matter, is it ever explained WHY the reapers/cerberus tried to "kidnap" the citade? were the reapers going to use it as some kind of instant whole planet harvester?
 * The Citadel IS the Catalyst, and as the endings shown, as soon as they attach the Crucible to it the Reapers lose. They weren't so much capturing it to use it as they were capturing it to ensure you couldn't instantly defeat them. In more meta terms, imagine how boring the game would have been if you battled long lines as you waited for the Crucible to dock uncontested with the Citadel, and then have a nice chat with the virtual boy before sacrificing yourself.

The Illusive Man move in elusive ways

 * Considering the absolute nigthmare it was to get to the teleport beam thingy while being supported by the entire military might of the milky way, how did TIM manage to show up for the final in the Citadel?
 * He was already long gone from the main Cerberus base when you showed up. In fact, he probably just went straight to the Citadel on a normal transport. Also keep in mind, he was indoctrinated, so the Reapers may have simply let him pass.

Sins of the Fathers

 * Can I ask why so many members of your squad have horrible fathers? This is really a series-wide question but Miranda, Tali and Jacob all had missions related to how their fathers were vile human beings (or Quarians) in Mass Effect 2 and Mass Effect 3 seemed to turn that up to eleven with Sanctuary. Likewise, James Vega mentions a dislike of his father and Thane was a bad father before he made the effort to redeem himself. Ashley and Garrus are the only ones who speak highly of their male parents and one of them was considered a traitor, if memory serves correctly.
 * You're thinking of Ashley's grandfather, who surrendered to the Turians at Shanxi (the alternative was to let them bomb the planet into the stone age). You also forgot Wrex (who had to kill him when he sprung a trap on holy ground). Anyway, the father I'm guessing is a relatively easy close relative to demonize. But don't forget we had Liara vs her mom, and Samara basically abandoned two of her daughters to kill the third.
 * For that matter, I can't think of any good fathers in the ME universe. Even Spacer Shepard seems to only have a mother. Bioware has father issues?
 * Anderson is a father figure, even referring to Shepard as "son" or "child", if that counts.
 * I was actually waiting for someone to mention Anderson so I could say, "No, he's a father figure, not a father." However, I did think of one after posting: Garrus's father seems like a good person. He listened to Garrus, and believed him enough to take the Reaper issue to the Primarch. The only problem I saw was that he insisted that Garrus not join the Spectres, but I think that he had a good enough reason for that.
 * Tali's father wasn't a vile person, just desperate and driven, and largely motivated by desire to give his daughter a chance to live on the homeworld. He did some very unwise and horrible decisions because of it, but his intentions were good. He just wasn't good at showing his emotions.
 * Well he was described as being the biggest war criminal in Quarian history and, if Tali's otherwise funny dialogue while drunk in Mass Effect 3 is anything to go by, she dislikes him by that point. She praises Miranda for killing her father, for example.
 * Even discounting the fact that he was a war criminal, he was an emotionally distant father, never took vacation to show his daughter his face, and used his dying words to give her orders. For comparison, another Quarian on the same ship got out a "Mommy loves you very much!" as the Geth burst in and killed her. Being emotionally distant is almost as bad as not being there.
 * At one point Shepard can ask EDI if she considers her creator as some kind of twisted father figure that causes her deep psychological issues. When she gets confused by this, he says he's learned he has to ask that kind of question.
 * Wrex's father was pretty shitty, too. Hell, he's probably the worst of the lot with the exception of Mr. Lawson. But anyway, this is lampshaded by a certain dwarf from another Bioware game; "Everybody needs some daddy issues."
 * Kaidan is on good terms with his father. So naturally he goes MIA fighting the Reapers.

Asari Biology

 * Ok So I romanced Liara as a male Shepard in ME 1 and reconnected in Lair of the Shadow Broker. I get that Asari use their meld to build a genetic template for their offspring but I am confused about the actual sex part. I assume that Asari have a vagina for actual birth but there would have been no reason for their biology to evolve compatible sexual traits and organs for sex with a human male. No pleasure center like the clitoris, no lubricant production to facilitate penetration, and so on. So how does Liara have traditional sex with Shepard? Or is it just a lot of making out and touching and Shepard's pleasure comes from the meld as well?
 * Yes. The real stimulation comes from the contact with the partner's nervous system. Both nervous systems become one temporarily, and both experience the same pleasure. Its probably not the same as you'd get from normal human-on-human sex. That said, much like normal sexual reproduction, asari evolutionary development would almost certainly go down the path of ensuring that the process of melding is highly enjoyable for the asari, which in turn would make it enjoyable for the partner.
 * There's also a reason for Asari to develop a uterus, vagina, and ovaries: Birth. They'd still need the egg to conceive the child, the uterus to house and grow the child as it develops, and the vagina to give birth, after all.
 * It's also possible that the Asari at one point in their evolutionary line were not a single sex species and that good old fashioned sex was the proto-Asari's means of reproduction. Then, as the proto-Asari evolved into a single sex species that can reproduce through the nervous system meld, they retained all of the biological traits associated with (pleasurable) sex. There would not really be nothing to select against clitorises (clitores?), self-lubricating vaginas, etc.
 * In the Asari temple, Javik specifically states that the Asari were genetically modified by the Protheans for their biotic abilities. This doesn't preclude modification in other ways, though, which includes their lifespan and reproduction methods. It's possible they had very different anatomy as a holdover prior to being modified, which is still useful for good old-fashioned sex. After all, when you walk into the bar on Ilium and meet Matriarch Aethyta, she treats sex casually, which seems unlikely if every sexual act is an intimate mind-meld.
 * "Can I get you anything? Sorry, no sex, I just cleaned the bar."
 * The flip side to this is also found in the bar on Ilium: the bachelor party conversation. All species seem attracted to Asari, describing different traits that only they can see. This brings up the possibility that they're only human-like to human onlookers, which suggests that they *do* mind-meld with everything in sight.
 * Except that all the participants of the bachelor party see things that everybody can see about the asari: the salarian takes notice to her attractive skin tone, the turian admires her head fringe and the human her body-shape, while all three are impressed by her flexibility. The asari look no different when you look them through covert video footage, so there's no way that they could influence the mind of every observer like that.
 * My assumption is that while you could engage in coitus with an asari, it wouldn't be as pleasurable for either party as what they consider "going all the way." Remember the krogan in ME2 talking about how eating a fish from the Presidium would be decadent, "like screwing Sha'ira" and his friend asks "where are you supposed to get a decent grip?" I took that to mean screwing an asari would be basically humping, rather than "embracing eternity." The decadence is beyond just some lowly mercenary bedding The Consort, but that you would schedule a meeting with her just to do something as crass as put your parts in hers rather than than meld nervous systems.

Legion and the Reaper Code

 * What does the code do and how does it allow the geth to achieve 'true' consciousness? What IS true consciousness? The geth as a whole seemed pretty to have a good grasp of awareness even if it was different from how organics think. What changed that the geth were no longer hundreds of programs interacting and is now an 'individual'?
 * The difference seems to be that, while a regular Geth program is non-sentient, the Geth as a whole only attaining self-awareness through the consensus, a single Reaper-upgraded Geth program is complex enough to be self-aware. Each single Geth program was upgraded to the level of EDI. Before the upgrade, the Geth as a race was self-aware, but each individual unit was not, they were basically a hivemind, now each unit is a "person".
 * Pretty much this. In order for the geth within a single platform to actually reach mental functioning comparable to a human, geth platforms must operate in large groups so that their network can handle basic functions more effectively and free up processing power for higher functions. Legion was unique in that they had enough geth programs within one specialized platform that they could operate independently. The Reaper codes allowed individual geth programs to become as aware as a true AI, letting them graduate from being simply VIs working in concert to actual individuals.
 * Well, if that is the case, then what happened to the ones inside legion, exactly. As I recall, he had over a thousand programs. If they are all still inside him, even if they are each complex enough by themselves to be their own individual, why does he refer to itself as "I" when there are still so many conciousnesses inside him? Furthermore, isn't it a bit of a cop out for him to accept the reaper code when the geth determined in the previous game that the reason they rejected the reapers is because they wanted to achieve their level of sapience on their own terms?
 * Legion uses the Reaper code because of the giant Reaper armada invading the galaxy, which is happening immediately after the quarians destroyed so many geth that overall operating capability within the entire Consensus was hampered to the point that the geth were reverting to baseline survival protocols. The geth don't have time to play around with developing their own tech at this point. The Reapers are here. They need those upgrades now.
 * We assume, sure. It's still weird Shepard doesn't have the opportunity to bring up the change in attitude, though.
 * I'm pretty sure that Shepard does/can bring it up to Legion and that his response is exactly what the person above you said - the Geth accepted the code out of desparation and that they were now under the influence of the Reapers because of the indoctrination that caused by part of the code and by the Reaper in their fortress (or whatever it is).
 * I would assume that the consensus now has the ability to implant individual entities in each Geth casing as seen fit which might lead to internal social climbing such as Geth soldier upgrading to Prime bodies. Originally, the Geth did not want the Reaper led change and so turned their back against it, but desperation and fear of genocide changed their moral imperative to survive. Once the change was incorporated, they were enslaved by the Reapers which leads to Legion's desperate cries to help him and his people. This helped their evolution and they couldn't turn their back on the possibility especially with the looming Reaper invasion. Mankind should never have evolved the atomic weapon but once the possibility was realized, we couldn't deny its allure. All life focuses on its evolution and its survival. The Geth are no different.

Exact number of Ardat-Yakshi

 * In ME2, Samara tells you that there are only three known Ardat-Yakshi in existence, which is reduced to two if you kill Morinth. However, in ME3, Banshees are revealed to be indoctrinated Ardat-Yakshi. When you first encounter them in Ardat-Yakshi monastery, it's mentioned that there are hundreds of Banshees running around the place, and you run into quite a few more as the game progresses. While Samara admits that there could be Ardat-Yakshi hiding out in remote areas, and that their abilities don't manifest until they reach a certain age, it still doesn't explain how the Ardat-Yakshi population just exploded in orders of magnitude in the couple of years between games.
 * Samara was lying. The Codex makes it clear that there are far more than just three Ardat-Yakshi. She's downplaying the number of Ardat-Yakshi because that's how the asari roll in general.
 * This doesn't make much sense, since she's a Justicar. She really has no reason to lie to Shepard at that point and "lying" doesn't seem to be something an organization as rigid as the Justicars would be very supportive of.
 * Based on what, exactly? We don't know the specifics of the Code. What we do know is that the Justicars' duties include containingng Ardat-Yakshi and that the asari as a whole have a vested interest in keeping the fact that Ardat-Yakshi even exist a secret. Samara would want to downplay the threat, if only due to species-wide social convention to hide the fact.
 * I don't think she was lying, she was just wrong - when she says there are three Ardat-Yakshi in existance, followed up by saying she has three daughters, before noting "It is as it sounds", she's clearly pretty cut up about it, the insinuation being she thinks she gave birth to the only three sex-vampires currently in existence. But after the suicide mission, I think, if Shep asks her what her intentions are, she indicates that there could be more out there, so she might go look for them. It's a little odd admittedly that she didn't know of the monestary full of them, including both her daughters who she talks to frequently, but meh. Minor retcon.
 * Maybe she was referring to fugitive Ardat-Yakshi?
 * No, it was pretty clear that she was talking about her daughters.
 * This troper seems to recall most of the inhabitants of the AY monastery being described as merely being "in the AY Spectrum," meaning that they have the genes necessary to proliferate Ardat-Yakshi, but were not "real" Ardat-Yaskh themselves. Only her two daughters are genuine Ardat-Yakshi.
 * Only problem with that is Samara has the genes necessary to proliferate Ardat Yakshi, and she's not in the temple, even though her Justicar code would've absolutely obligated her to live there. But different levels of Ardat (as someone's suggested below!) works for me. T'Loak's heard of 'em, and isn't surprised by the fact that they're more than just a myth. Samara might have given birth to the only three true Ardat-Yakshi, but if we've got a few half-Ardat kicking about, we can bung them in the monastery too.
 * The impression I got from the codex entry was that there are different "levels" of ardat-yakshi; only the most severe cases, such as Samara's daughters, cause death via melding. Most just cause extreme pain and possible brain damage. Samara might have been counting the ones who have the potentially lethal version for simplicity's sake.
 * That's the impression I got, too, and the Mass Effect wiki (though by no means infallible) supports this interpretation.
 * I simply looked at it as the Reapers altering the genes of a normal Asari to make them an Ardat-Yakshi. After all, they can blend a Krogan and Turian to make a husk, and a Batarian and Human, how hard would it be to turn an Asari into an Ardat-Yakshi before huskifying her?
 * This is probably one of those "Do you want the in-universe answer or the real answer?" kind of things. i.e. they wanted a level set in a monastery built to house a psychic sex vampire commune that is currently overrun by zombies and couldn't do that with just two of them left, so they retconned. Either that, or Samara was trying to hide just how common AY's really are, whatever floats your boat.

Reapers attack on Sanctuary

 * If the reapers have the Illusive man in their pocket via indoctrination, what is the point of their attack on Sanctuary?
 * They attacked at the point where TIM's research into Reaper control mechanisms got far enough that they believed he could end up becoming a threat. The real question is why they thought that if an indoctrinated person could not take control of them.
 * "Indoctrinated" does not mean "absolutely and totally under their control." TIM was indoctrinated to the point where he was useful if manipulated with subtlety, but he could still act overly on his own if he wanted to. Besides, the facility as a whole was a threat regardless; if the Alliance or any other galactic power found Sanctuary, they could use the research just as readily as Cerberus.
 * The man running the place for TIM ISN't indoctrinated.
 * TIM's investigation of Reaper code leaves a trail that could make the war more difficult for Reaper armada. He is leaving bread crumbs which will help others if not stopped. Just like Saren left bread crumbs which enraged Sovereign: the beacon, the Thorian, the Krogan facility on Virmire. Humanity has found a hero that gets those bread crumbs and uses it against the Reaper agenda, just like he did with the crumbs those damned Protheans left behind and also the secret weapon passed down through countless cycles and kept secret each time. The Reapers don't want peace, they want dominance. Anything else is a nuisance.

"They used to eat flies."

 * Concerning the secret squad member: When it's pointed out to him that salarians are a major player in galactic politics, Javik acts surprised and remarks that they were only animals during his time. The question is - how does he know what a salarian is? How does he recognize a term that presumably did not exist 50,000 years previously? This is something that the Universal Translator could not possibly handle. The only possible explanation I can think of is that salarians already had a primitive culture back then and already called themselves "salarians," meaning that the Protheans ate a sentient species...
 * Maybe the fact Javik doesn't use a simple Universal Translator, but actually interfaced with a sentient mind (Shepard's) to learn the language has something to do with it. Like, it connected whatever word the Protheans used for "Salarian" with the current name of the species, based on the memories in Shepard's mind correlating to the primitive species that existed back then. This, of course, raises the question of why he was surprised at all, since he should have already known Salarians were one of the dominant species of the cycle at that point.
 * Javik doesn't use a universal translator. he doesn't need to. He reached out, he touched Shepard's mind, and bam. He knows everything he needs to know to communicate with Shepard, including current names of species.
 * That'd be a perfect explanation, actually, but then there's the fact that he misidentifies them as lizards instead of amphibians and has to be corrected...
 * He has trouble comprehending how "primitives" could have evolved so much. It's not a stretch to say that salarians really were lizards back then and just evolved into amphibians, and the reality of such is difficult for Javik.
 * Alternatively, he simply doesn't care about the difference between a reptile and an amphibian; he's not a biologist and his point isn't biological, it's that in his time, they were slimy, non-sentient to barely-sentient bug eaters. Frog, lizard, doesn't matter. The fact that they got from what and where they were to what and where they are is what he finds shocking.
 * Javik says the Protheans used to eat Salarian livers as a delicacy. So it makes as much sense for them to know what a Salarian is as it makes sense for us to know what a pig is. And indeed we would be very surprised that if we came back to earth after 50,000 years, there would suddenly be an advanced civilisation of pig-men.

Neutral Options
Why does the dialog wheel never have neutral options anymore? It's always straight Paragon or Renegade now. Did just no-one ever use them so they didn't bother recording them or what?
 * It's in part because people literally almost never used them, but also because Bioware has been slightly stepping away from pure Paragon and Renegade in the standard options anyway. In many, many occasions the lower option isn't any more pragmatic or Jerkass than the above, just different in content. Only the red and blue options still represent Paragon and Renegade at their purest, any more. In any case, it's a question of resources: record dialogue that is the least satisfying to watch, that few use, or record greater amounts of actually interesting dialogue.
 * There was generally no point behind a neutral option; neutral options gained you neither Paragon or Renegade points, so they were functionally useless and no one used them. They could have gone with the Dragon Age II system and had the neutral option be sarcastic/humorous, but there still likely would't be any point to it.
 * There's also the fact that most "paragon" and "renegade" dialogue choices don't net you paragon or renegade points - they net you general reputation points. There were a lot of times when I was giddy at being a jerk-ass to someone only to see the combination symbol bounce up. Of course, I was still happy about it, because the dialogue is more important than the points you get.
 * War is a very polarizing experience, and right now you're in the middle of the biggest one since the Protheans and the Reapers were going at it a cycle ago.

The definition of "synthetic life"? *ENDING SPOILERS*

 * In one of the three endings all synthetic life in the galaxy is destroyed. The problem is, how do you define "synthetic life" as a concept? The Reapers function in a manner extremely different from the geth, and both bear only passing resemblance to EDI's architecture. So are we to infer that this ending destroys, not just A Is, but also V Is, computers, pocket calculators and coffee makers? The Catalyst may be hyperintelligent, but it's doubtful it can direct the signal individually to every sentient synthetic in existence; there must be collateral damage.
 * Not only that, but if the Catalyst could target any synthetic life-form, why couldn't Shepard brow-beat it into targeting the Reapers and only the Reapers, making the "Destroy" option much more appealing?
 * Brow beat it how? The Catalyst holds the cards, and it knows that. It wants Shepard to destroy all synthetic life. Its in a dominant position and is no more susceptible to persuasion than any Reaper.
 * How about the fact he wouldn't need to brow beat it, since the Reapers have been established to have their own unique code then any other synthetic life thus far. It's like comparing a cell phone from today to the very first cell phone ever created, the Reapers are just a super duper advanced computer program. But a distinctly different program from all others none the less. This has been established so many times throughout the series it isn't even funny how huge a plot hole it rips open in these endings. If this Catalyst has the ability to rewrite DNA, it can specifically target Reaper code instead of just a broad sweeping encompass of all synthetic life! This is especially glaring considering that if you don't have enough war assets, it ends up wiping out organic AND synthetic life, meaning apparently if you have enough war points the thing could be specific enough to only target synthetic life, but you'll never have enough to only target the Reapers. In a word: Bullshit!
 * You're missing the point. Yes, the Cataylst can be that specific. But it doesn't have to, and it doesn't need to. Its pretty much in complete control of the situation. Shepard has to play its game, and as annoying as that is, that's the situation Shepard is in at that point.
 * The Catalyst never gave off the impression that it was attempting to be that controlling - rather it more or less said "Hey, here are your options. Pick." and left it at that (Yes, Shepard could have enquired further and gotten more out of it but that's a whole other issue). At that point, the Catalyst very much seemed like it'd do whatever Shepard asked, up to and including having the Reapers bugger off and letting life continue, potential-future-synthetic-war and all (the complete opposite of its dedicated function) as it fully admitted its way wasn't going to work anymore. So if as you say it could be that specific, there's no reason to see why it wouldn't have been.
 * Well, all synthetic life in this cycle seems to have a "touch" of Reaper anyways. EDI was made by improving the Luna AI with Reaper tech, the Geth get Reaper upgrades... I wouldn't be surprised if even Shepard had a little Reaper tech in him, from the Lazarus Project.
 * And yet Shepard can survive. Insert sarcastic remark here.
 * "A stubborn enough person can survive just about anything."
 * The Catalyst can control the Reapers; we know that because he says it and you take control of them in the "Control" ending. If having some Reaper code made you the same as the Reapers, then he should be able to control the Geth and EDI as well. As he can't (and Shepard doesn't, in "Control"), we know that there is something differentiating the various synthetics. So how exactly does unleashing the Catalyst destroy all synthetics? It isn't some sort of EMP wave, because non-sentient technology--even that influenced by Reaper tech, like the Normandy--is just fine. Either the Catalyst can differentiate between synthetics but just doesn't (possible, but frustrating as Shepard can't even try and argue the point), or else this is just forced into the "Destroy" ending to make it seem less obviously the correct choice. I'm going with the latter.
 * You aren't flipping a switch or pulling a trigger; the destruction ending is shooting a pipe and blowing something up. You are causing a catastrophic failure in the catalyst/cruicible; what you're doing is not an intended design mechanism. The fact that it is as targeted as it is(synthetics) is nothing short of a miracle.

Male divinities in the asari pantheon?
In the Temple of Athame we see statues of male angel-equivalents who were credited teaching the asari about civilization. Shouldn't this have ringed some bells in the heads of every anthropologist in existence concerning the origins of the asari culture? Where would they have learned about the existence of masculine entities at all, outside alien contact?
 * Revisit the Temple with Javik in your party. The asari probably got the idea for male divinities from the protheans. As for why that didn't turn any heads, this information was probably kept hidden by the asari government, same as with the Beacon/Prothean VI hidden in the Athame statue itself.
 * I know the Prothean connection just fine; the question is why no outsider picked up the fact that an all-female species has male angels in their religion. You can't hide a component of a major religion from the general public.
 * Liara mentions that the many don't follow the Athame doctrine in recent times and given the secrecy surrounding the temple, it's likely they prevented outsiders from entering it based on religious/traditional principles akin to how no non-Muslims can enter Mecca.
 * Liara also mentions "Athame's" image became "more Asari" over time when you look at the central statue. The Prothean depiction of those entities is probably very old (as are the artifacts on that temple), maybe pre-spaceflight even, and current Asari population simply believes they all looked like Asari, or at least somewhat Asari-like. What really seems wrong to me is how that Prothean VI was very much aware of the Reaper threat, was supposed to help people fight it, and yet the Asari are completely oblivious of the existence of Reapers before the events of the series. How did they get any information out of that beacon without triggering the activation of Vendetta?
 * The same way human beings got information out of the Mars Archive; decoding it from the raw bits one laborious piece at a time. Vendetta suffered the same flaw as other Prothean beacons did of requiring somebody with the ability to do the Prothean meld-communication to fully activate it, and doing that requires either the Cipher or being a Prothean. So Vendetta never activated until you showed up.
 * Of course, if the maker of Vendetta had programmed the thing to be even half as user-friendly as Vigil then yes, the asari would have been leading the galaxy to start anti-Reaper prep starting like 3000 years ago. Sorta an Idiot Ball there, Vendetta engineers.
 * Vigil was designed by a completely different group of Protheans. Javik is surprised to hear about its presence on Ilos, and the Prothean voice recordings - "Can not be stopped! Can not be stopped! - seem unlikely to have come from Javik's strain. It could even have been a completely different species in the Prothean empire. The light they flung into the future might have been modified by the few members who survived the wait and were revived. Just the fact that they modified the keepers to not be treacherous, but kept them around, proves they thought differently.
 * And there are real, human religions with half-animal, half-human divinities (for example). So by your logic, the fact that the Egyptians had Ra and Anubis as gods would throw up a red flag since there weren't actually bird-people or jackal-people. Hell, humans even have gender/sexless divinities (the Christian God has no gender for example). The Asari probably knew what males were (unless every other species on Thessia is also only feminine gendered or agender), so they could imagine male divinities.
 * I just think it's weird that Liara, or any other Prothean expert, would never have figured out that the busts of Athame's followers were of Protheans. While the audience only learnt what Protheans really looked like in ME 3, there's no indication that Javik's appearance was surprising to the characters, and it's hard to believe that no-one knew what the Protheans looked like with all those ruins lying about the galaxy. If the busts had been kept hidden, then sure... but Liara recognised them instantly.
 * Well, the Codex entry on the Protheans (before you meet Javik, at least) still shows the tentacle-faced statues on Ilos. It's possible that some asari scholars attributed the busts to some alien race, but nobody (outside of the Athame doctrine, which also knew about the Beacon) could confirm they were Prothean until they found one to compare them to.

Reaper Tech and Indoctrination
Isn't anybody worried about people in the Alliance, Council, or other races being indoctrinated during the main story? The Reaper tech you picked up during the N7 Sanctum mission goes straight to Alliance researchers and nobody thinks that might be a problem? The Derelict Reaper from Mass Effect 2 proved that Reaper corpses with any kind of power can still generate enough juice to indoctrinate organics ... yet nobody seems to be bothered by giant Reaper corpses now sitting on Tuchanka and Rannoch?
 * The small Reaper devices are likely safe; the only Reaper devices encountered that caused indoctrination are large-scale objects like Reaper themselves, Object Rho, and the device in the mine. As for the dead Reapers on Tuchanka and Rannoch, those would likely be disassembled - explosively - and the areas around them would be marked as no-go zones until the Reaper is completely destroyed. Remember that once Sovereign was destroyed, there was no danger of indoctrination on the Citadel from the wreckage, and the derelict Reaper was still largely intact with a functional power core. The Reapers disabled on Tuchanka and Rannoch were completely destroyed with no intact power supplies, and indoctrination fields can only exist if the Reaper is still getting power and is intact, and both of those Reapers were very much not intact by the end.
 * In the Shadow Broker files it's discussed how some Reaper tech is being analyzed from distance using remote drones to avoid the Indoctrination effect. Most likely all these objects are treated as extremely hazardous materials, and no-one will approach them in person once they've been secured.
 * Even if they are isolated, if they are still capable of indoctrination the wreck on Tuchanka is right in the territory of the mother of all Thresher Maws. Imagine that thing being indoctrinated or huskified...
 * Again, if the Reaper tech is sufficiently damaged then it cannot indoctrinate. The Reaper's power core needs to be active to generate husks or indoctrination fields, and if Kalros inflicts sufficient damage to the Reaper, which is indicated when it attacks, then the Reaper will be completely inert.
 * There is no indication of how damaged a Reaper has to be to lose its indoctrination field; judging from the Derelict Reaper they don't have to be in a sapient condition do cause the effect. However, even if the field continues to excert influence, I doubt that a creature as simple as the Tresher Maw could be affected; it's not the type of creature to understand the complex ideas that the indoctrination influences on; at best a Reaper could guide it to attack specified targets, but since the Reaper is dead, there is nothing Kalros is likely to do besides what it has always done, which is to guard its territory.

Scions and Praetorians
Why the absence of these enemies? Being made from Husks, there should be plenty of materials on hand for the Reapers to make more of them, and we know that the Scions, at least, are not Collector-dependent, as they show up on the Derelict Reaper.
 * Ravagers do the same job as Scions with greater mobility. Pretorians's limited effectiveness against Shepard's team likely resulted in them being phased out; Harvesters do a better job overall as close air support platforms.
 * Bigger question on my mind is where did all the mechs go? You'd think that with the Reaper invasion they'd be in higher demand than ever. Hell, they'd make perfect canon fodder for TIM's army.
 * Considering how unreliable they proved in the previous game, I wouldn't be surprised that TIM just refused to use them to guard critical installations, let alone have them deployed on strike ops.

War Asset oddities
Much of the process of gathering war assets seems completely arbitrary. Why are there random warships and commando teams hanging around planets without either reaper presence or installations to defend? Why was the Volus dreadnaught Kwunu orbiting a random gas giant instead of defending the homeworld or linking up with other fleets? It is also possible to gain Asari assets before the invasion of Thessia that are for some reason NOT recalled to defend the homeworld.
 * Units separated from the main fleet without orders to move due to comm buoy disruption. I always viewed it as simply being a case of Shepard finding the unit/fleet, and relaying orders for them to link up with the fleets they got separated from. As for why they're in such out of the way places, just about all of those systems are in Reaper-controlled zones. They're likely hiding out for fear of being detected and destroyed/harvested, and unlike the Normandy, they don't have a stealth system to hide their presence. Normandy can give them a link to their respective command via their QEC and can give them an opportunity to get to the main mass relay and get out of the system and occupied cluster.
 * Or you store the warships in pokeball-like devices in your cargo hold.

Why were the Keepers and Saren even necessary?
If the Catalyst is the Citadel, why couldn't it have just activated the relay itself? Why bother with the Keepers and after they failed, sending in Saren and Sovereign to activate it manually? I mean, christ, that combined with TIM being a recycling of Saren makes me wonder if Mac Walters knows a damn thing about the series lore.
 * All indications are that the Catalyst does not directly control the process. It set up the cycle and then simply sat back and let things progress on their own. The Reapers and their cycle are an autonomous process that it doesn't oversee. Besides, if something came along that broke that cycle, the Catalyst is perfectly willing to accept that.
 * The problem with that idea is that his ENTIRE EXPLANATION of the relationship is "The Reapers are mine. I control them. They are my solution".
 * Which is very vague and non-specific. Observed behavior from the Reapers make it clear that the Catalyst, despite being in overall control, is hands-off and doesn't direct the Reapers itself. It could, theoretically, have intervened if it chose to, but it chose not to intervene in the Protheans' plan and the subsequent struggle against Saren.
 * Which choice would have Orcus On His Throne marrying the Idiot Ball, which was the entire complaint in the first place.
 * This has been mentioned in the WMG for 2, but there's also the fact that even with the delay in the Reaper arrival from, well, Arrival, it apparently takes the Reaper fleet less than a year to reach Batarian space from wherever they're hanging out in dark space. For a species who have been around for tens of millions of years (at least), this is nothing. Why bother activating the Citadel Relay to dark space at all? If all it takes is a couple of months, why doesn't the Reaper fleet just mosey on over to the Alpha Relay when it's good and ready and take everyone by total surprise that way? Particularly once the Protheans disable the Keeper signal.
 * It actually took them over a millennium to reach Batarian space from wherever they're hanging out. Remember, Saren and the Geth were not Sovereign's first attempt at solving the problem with the Citadel Relay. The genocide signal's been active since earlier than the rachni war.

Why did the Reapers wait to attack the Citadel?
They couldn't get a vanguard in to bring the whole fleet down at once, but Vigil told us the core of their strategy in his time was capturing the citadel and locking down the whole Mass Relay network so that every system was isolated and they had access to the Empire's full records of every planet and species. I can't think of any reason they didn't even attempt it until the off-screen attack at the end of the game. Well, except that it would have worked and Shepard's mission would have failed before it began. Admittedly, there is a single problem with that theory: Later, the Reapers seemed able to get into the Citadel without problems. I would guess that there was another attack from inside the Citadel, perhaps by sleeper agents, perhaps by TIM, that gave the Reapers some control over the Citadel. I didn’t miss it. I specifically said that the claim is shot to pieces when the Citadel goes dark and NOBODY comes to its rescue. As I said, it’s Show Don't Tell: if we’re supposed to buy that a large number of fleets are on “standby” to come running if the Citadel is in trouble, why are YOU the first person alerted and the only one who shows up to help when there’s even a HINT of trouble at the Citadel. As I mentioned before, if NORAD or the Pentagon went dark in real life, the US military would mobilize every available unit to figure out what the hell happened, and WE’RE not even at war. The argument of “it was assassination, not outright war” is BS. It was a SIEGE; even if assassination was the goal, they still CAPTURED the Citadel. Again, Show Don't Tell. What you're saying is speculation based on out-of-context rationalization. But this is a BIG plot element because it was the entire FOCUS of the first game. It needed to be addressed directly, not hand-waved or speculated. As for the “we don’t know how much of the Citadel is Reaper-operational” theory, that is still a crappy explanation. It renders the entire plot of ME 1 moot (as it destroys the tension and purpose of Sovereign’s attack) and it’s once more something that should be SHOWN.
 * Because it wouldn't have worked. The Citadel has the ability to close its arms, making access impossible. It's unlikely that the Reapers would want to risk destroying it, seeing as it houses their boss (which they may or may not know) and the key to the next successful invasion (which they definitely do). It may even be that it is literally indestructible. Plus, attacking the Citadel would have instantly rallied every council race under one banner, since they're fully aware of the Citadel's strategic importance.
 * Why would they want to attack the Citadel? Everybody and their dog is fleeing to that place from the invasion -- a place that was in no way hidden, that they know better than anyone. It's a perfect set-up: destroy the civilizations, let the refugees flee in one place where they can be easily mopped out in the end, instead of scattering all over the galaxy into tiny enclaves. Three guesses which is more efficient solution in terms of completing the harvest in least time with least energy spent.
 * Because in the first game it was established that they can shut down the entire mass relay network from the citadel, which prevents the races of the galaxy from gathering enough forces to present a legitimate threat and traps them in whatever cluster they happened to in at the time. In other words, they could have easily averted the entire game and effortlessly won the war in one strike. At the end-game they take it so easily that it happens off-screen and is over by the time word of the attack gets out. They still don't close the relays, but this may be to bring all the fleets into one doomed battle (even with them all together they can't win without the Crucible) or a final test by the Catalyst.
 * The difference is that in previous cycles nobody knew the Reaper's were coming, so taking the Citadel allowed them to plunge the galaxy into chaos. This time around Shepard found out about them and put a stop to them, so they don't have that advantage anymore. If they shut down the relays the local forces there would know what was going on and could just mine the entrance to the relays, or kill themselves to stop the Reaper's using them to make more Reapers, or any other scenarios that would inconvience them. They don't shut off the Mass Relay network because leaving it open gives the organics hope that they can win, allowing the Reaper's indoctrinated agents to deal with them and get them into a position that suits the Reaper's purpose.
 * All the ideas above likely have some bearing on the decision not to attack the Citadel. Remember, the final assault was after the the Alliance might have recovered a way of taking control of their husks, which understandably seems to have worried them. There's also the fact that they've just wiped out the homeworld of the last major species, meaning their plan and take out the last remaining major centre of government makes sense at this point.
 * Technically, the Reapers did try to capture the Citadel early on. Cerberus attack, anyone? They were surely indoctrinated by that point, and it's possible Udina was as well. It seems the Reapers wanted to avoid a direct assault on the Citadel (probably to avoid the risk of destroying it as mentioned above), but must have deemed it necessary after they found it's the final piece of the Crucible.
 * Which doesn't make the situation any better, because they were able to move it without harming it. If that hadn't happened, we could have assumed that the Reapers felt it might be too costly. But after they just waltz in and take the thing, it only makes their earlier precautions seem like overcautiousness.
 * By the time they "waltz in and take the thing", they have thoroughly exhausted galactic defenses. The Reapers spend the entirety of ME 3 pulling a Divide and Conquer war; keeping the various races separated by forcing them to focus on defending their own worlds. If they'd attacked the Citadel at the start, the combined forces of all the races of the galaxy would have come together to defend it. Instead, by the time they attack the Citadel, the turians are exhausted from the war on Palaven, the Alliance is busy trying to not get exterminated on Earth, the asari homeworld is destroyed, the geth and quarians have weakened each other with their pointless war, Citadel Security's been put through the ringer by Cerberus, etc. etc. And whoever isn't wiped out is busy halfway across the galaxy building the Crucible. The galaxy at that point is weak enough that there's nobody left to put up a fight when they stroll in and seize the Citadel.
 * That's base speculation. For one thing, before the game even starts, we know that every species was too busy defending its own territory to help do anything else. It isn't until you show up and personally solve their problems that they even have a fleet to spare (or, in the case of the quarians/geth, have a fleet at all). By the time the Reapers actually show up to take the Citadel, they're not pushing against a weakened galaxy--because the galaxy was at its weakest before Shepard began gathering allies. The point where the Reapers take the Citadel is specifically to protect it from the forces Shepard had just gathered.
 * Only if you assume that nobody has been dying in the wars that have been waged between Reapers and everyone else in the time that Shepard's been gathering allies. It's made pretty clear several times that people are throwing more and more support behind the Crucible because as the war wages on, everyone's dying, all the defensive forces people have are being wiped out, and what started as a silly "You want me to throw my forces at your plan when I have my defense to think about?" is instead rapidly becoming the only hope anyone has left. Getting allies for the Crucible was difficult because as far as anyone else was concerned, it was just a human project to defend Earth, and they had much larger priorities to think about (namely, saving their own worlds) to care about what they perceived as Shepard's selfish plan to ensure the survival of his own planet at the cost of everyone else. If the Reapers had hit the Citadel instead, every race has a stake in that and would have thrown their immediate support into defending it.
 * And again, that is a severe violation of Show Don't Tell. Furthermore, that has nothing to do with how the Reapers come in and take the Citadel earlier. Show us that the Citadel is being constantly defended. Show us that the other races are willing to drop whatever they're supposedly doing in order to come to the Citadel's aide. When the Citadel goes dark during the Cerberus attack, only Shepard, who happened to be there, did anything about it. If the Citadel was being so rigorously and staunchly defended, where were the council races' reinforcements? How come the Salarian councilor comes to you instead of the fleets you're speculating were ready to come to their aide? Even if we assume that they were waiting for a full-on attack rather than an attack from within, Cerberus didn't even put up a pretense that things were working normally. In Real Life, if NORAD went out of commission for even a few minutes, the entire US military would effectively lose its mind. We've actually almost gone to nuclear war several times in the past because of this. And lastly, even if we assume people have been suffering heavy casualties or whatever throughout the war, there's no reason why none of those fleets still wouldn't be defending the Citadel to their dying breath. That's where their seat of government was, and we know for a FACT from the first game that if the Citadel fell, the Reapers would control the relay network and everyone would be screwed. So, with all of that in mind, no--that plot point still fails.
 * You missed the point. I never said that there ARE huge fleets defending the Citadel. I said that there WOULD BE huge fleets coming to the rescue of the Citadel as soon as word hit the extranet that the Reapers were bombarding the Citadel and killing everyone. It would stir up a hornet's nest that would bring the fury of the galaxy to bear against them. One guaranteed way to unite a divided people is to threaten something that all of those people love, and in this case, that is the Citadel. This changed as the war dragged on, because there wasn't much left to defend with. The Asari councilor even says as much when she talks to Shepard after Thessia falls; that the Crucible is their last hope. When Shepard tells her that the Crucible can't work without the information Cerberus stole, she loses hope and starts talking about "continuity of civilization".
 * As for the Cerberus attack earlier, that was rather explicitly an assassination attempt, not a conquest. Assassinating the Council is one thing; successfully conquering and then holding and defending the Citadel against a united fleet is another thing entirely. The Reapers are only really capable of precision strikes like that through indoctrinated agents, such as Cerberus. An assassination attempt by terrorists does not merit pulling the fleet away from their respective warzones; it's what Citadel Security and agents like the Spectres exist for. An armada of Reapers showing up through the Widow Relay and attacking the Citadel is on a completely different threat scale than Cerberus.
 * Finally, as to the point of shutting down the Relay System, that also gets back to Show Don't Tell; as it is, we've never actually seen this. We've only been told this is something they can do; at no point in the history of the series has the Reapers' ability to disable the Relays ever actually been used as a plot point in modern galactic civilization. As we do not know the full extent of what the Protheans did when they sabotaged the Citadel, we don't know how much of the Citadel's Reaper functionality is operational, or how long it would take to bring such functionality online. Supporting this point is the fact that, as many have decried, when the Reapers DID take control of the Citadel, their vaunted ability to disable the the Relays was still never implemented; the Crucible and the invading fleets came through just fine. People have argued back and forth about WHY the Reapers didn't shut down the Relays, when the real question is whether or not they even COULD. They could before the Prothean sabotage, but for the modern conflict, we've certainly never seen it.
 * Again, I never said anything about a large number of fleets being on "standby". There are no such standby fleets. There are, however, many fleets engaged in combat with Reapers that could be pulled away to defend the Citadel if the Reapers had focused their attack there instead of spreading out their forces to engage everyone simultaneously. Best case scenario, they would succeed and take the Citadel, and the martyrdom of the Citadel would be the rallying cry that unites the entire galaxy in a single move. The original plan of taking the Citadel as the first move of the war only works because it's a surprise attack; without the ability to blitzkrieg the galaxy during the chaos caused by the loss of the leadership, taking the Citadel means nothing. Without that, there is no gain in conquering the Citadel except for a Relay-disabling ability that has been PROVEN not to function properly.
 * Not everything needs to be shown. Some things can be assumed, and the Citadel is one of those, because that point was NOT the focus of the first game; the Citadel's ability to disable the Relays has nothing whatsoever to do with the first game at all. The only time it was ever relevant is in how the Reapers conquered the old cycles, and that method was closed to them as a result of the first game. The focus of the first game was the Citadel Relay's ability to bring the Reapers out of dark space and into Citadel space for a surprise ambush that kicks off the war by destroying the leadership. Preventing them from popping a surprise war on an unprepared galaxy, wiping out the Council, and following through with the immediate extermination of everyone else was the central focus of the first game. The only reason the war in ME 3 is anything less than a one-sided curbstomp is because the Reapers were delayed, and because technology like the Thanix Cannon that would not exist without the reverse-engineering of Sovereign is now available. Had Sovereign succeeded in opening the Citadel Relay, rocks would fall, everyone would die, and ME 2 and 3 never would have happened. I do not see how the fact that they never take advantage of the "disable the Relays" functionality we've only heard mention of here and there in any way invalidates the fact that if Sovereign succeeded, the war would be over before it began.
 * Those are called "standby fleets". A fleet that could be pulled away from somewhere else to come to the Citadel's aid are standby fleets. Let's not be semantic here. And this assumption that destroying the Citadel would be a "rallying cry" is speculation, again. You don't know what would happen anymore than any other fan. For all we know, destroying the Citadel could affect morale. And finally, where in the series is it stated that the Relay control doesn't work? Who said it? When is it said?
 * And yes, it NEEDS to be shown. Because the Conduit was the main MacGuffin of the first game. The entire point to Sovereign's plot was to get Saren in the Citadel to keep it open long enough for Sovereign to open it and call the Reapers through dark space. Then, we're explicitly told that the Reapers would cut off the leadership of galactic civilization and shut down the relay network. The last two things are still very powerful tools at this stage in the war, surprise attack or not. Claiming that shutting down the relays wouldn't be effective without the ambush is like saying destroying supply lines wouldn't matter in Real Life conflict. And again, the scariest thing about the Citadel is that it isolated entire star clusters from each other. Cutting off the head of governement is brutal yes, but the Reapers then had the ability to isolate and destroy each cluster one by one at their leisure, since only they could use the Relays. Nowhere does it state in the narrative that this was disabled, and even if it was, that makes stopping Sovereign somewhat less meaningful.
 * And nowhere in the narrative is it ever suggested that the Relay control still functions, either. You keep throwing Show Don't Tell around, but we've only ever been told that the Citadel can do that. When have we been explicitly shown that the Citadel still possesses this functionality? Even when the Reapers controlled the Citadel, the Relays worked just fine. If the Citadel truly possesses the power to disable the Relays, why didn't they? Because we don't know the full extent of the Prothean sabotage, anything and everything that we have been told the Citadel should be able to do should not be assumed to be something it can do if we never see it for ourselves.
 * No, but we were told that was the Reapers' goal. That's part of what they used to defeat the old cycle. So, we know it happened--therefore, if something changed, you have to demonstrate that it changed, not speculate it. Claiming, "But they never said that X did/didn't happen" is the creed of Fan Wank theory.

Vendetta (Prothean VI)
Vendetta was programmed to reveal the Citadel as the Catalyst only once the Crucible was completed. He explains this is to avert the Reapers’ learning of the threat in advance and then taking control of the Citadel to prevent the Crucible’s use. But isn't “taking control of the Citadel” usually the very first thing the Reapers do? Why would he have been programmed with safeguards that assumed otherwise? The only Protheans with reason to believe the following cycle would prevent the Citadel-trap were the Ilos team, and they worked in complete isolation. Are we meant to assume the Citadel is normally left undefended after the Reapers make use of it?
 * They were probably hoping that the next cycle would actually find and pay attention to their Beacons, and as such start preparing well before they reached the 50,000-year deadline.
 * Pretty much. Javik was outright shocked that when a beacon was uncovered, that no one heeded their warnings. They thought that the beacons would serve as a perfectly functional warning.
 * Fair point. Though if the assumption was that the Crucible would be developed sometime before the Reapers even arrived, it makes even less sense to program Vendetta to withhold information on the Catalyst for the reasons it offered.
 * The only flaw in their cunning plan, then, was to assume that the Beacons would make it through intact in numbers greater than 1, and/or that anyone would actually find them before the Reapers start to send in Indoctrinated minions to destroy the evidence before it can be analyzed and disseminated. Probably should have left a couple near the worlds they KNEW sentient life was developing on...
 * They did. That's exactly why they left a beacon on Thessia in the first place: the Protheans were convinced that the asari would be able to stop the next phase of the cycle. And more than one beacon did survive into the next cycle. The one on Thessia, the one on Eden Prime, and the one on Virmire.
 * Javik is pretty honest, at least with a cynical Shep, about the fact he's lying to keep Liara's spirits up. More importantly, ME 1 told us that the warnings were sent out to the beacons by the Ilos team after the Reapers had returned to dark space. Though it's not especially implausible to think disparate groups of Protheans had the same ideas.

The Reapers' Rachni Queen

 * Two questions here: why was the Rachni Queen able to resist the effects of the Reapers' indoctrination? Also, she made it clear that if she had any more children, they would be able to help build the Crucible, so why were they immune to the effects of the Reapers' indoctrination when the Ravagers she'd given birth to before were more than happy to attack everything in sight?
 * Those Ravagers were heavily roboticized, so I'd say we weren't looking at Indoctrinated rachni so much as huskified rachni. As for resisting Indoctrination, no idea. Maybe a prepared Hive Mind can fend off Indoctrination (that is why the saved queen can help you, while the new queen if you didn't save the first one betrays you the first chance she gets).
 * Remember in the first game where the Queen tells you about "the ones who soured the songs of our ancestors". That creepy Russian scientist guy also said that the Rachni Queens are born with all the born with the memories of their fathers/mothers. I just assumed that the Rachni Queen you save had the memories of what was done to her people and had the time to figure out a way to dodge being indoctrinated.
 * The queens can probably resist indoctrination, but lesser rachni like workers, soldiers, and brood warriors can't. If what happened to the rachni queen is any indicator, Sovereign took control of various nests' lesser rachni and imprisoned the queen, using her to breed more warriors.
 * I think we can chalk it up to a mix of Genetic Memory and Hive Mind. Rachni queens carry the memories of their ancestors, which might give them a resistance to indoctrination; on top of that, their Genetic Memory also seems like an offshoot of their Hive Mind, and it's shown elsewhere that a Hive Mind is capable of preventing indoctrination from taking hold. It's what allows Shiala, who still is indoctrinated, to not be overcome by the Reapers' will. The rachni enemies that Shepard encounters are all husks, which are a mix of organic tissue and synthetic material because of Reaper interference. The Queen herself is still fully organic, as are the children the Queen produces after being freed.
 * We get at least a hint, if not outright confirmation, that hive minds are inherently resistant to indoctrination from Shiala. Assuming you helped Zhu's Hope out previously, she sends you an email revealing that they are fighting the invasion effectively because the Thorian's implantation has linked their minds permanently, and she also admits that she is still indoctrinated. I don't recall her exact words, but it is something along the lines of she is able to hear the Reapers' whispers, but the voices of the Zhu's Hope colonists are stronger and so the whispers can't affect her. As a result, it is safe to assume properly networked Rachni have an even stronger hive mind and are thus even more resistant to indoctrination. As for the queen herself, recall that Benezia was able to fight off indoctrination briefly. As the head of an absolutely massive hive mind, I for one think it is safe to say that Rachni Queens are by many orders of magnitude the most powerful-minded beings in existence, surpassing probably all asari matriarchs combined. The Queen from Noveria seems more annoyed and dismissive of indoctrination when we encounter her in 3 than concerned by it, and knowing how strong indoctrination is, any being that can consider it to be merely an annoyance is frighteningly powerful.

"Chemistry of Life"

 * I understand that in this day and age, biology is the go-to magical science, but how does Javik's "biochemical touch" even work? How does it distinguish between neurotransmitters and hormones of various unrelated races, allowing him to detect their feelings? How can he detect traces of Grunt - and his emotions - in the cargo hold, after the entire spaceship has been refitted and presumably UV'd, scrubbed and chemically cleaned to oblivion? Why not use something like "individual biotic aura" for Javik to feel? Biotics are already well-established within the ME universe and, at least for me, would be much easier to swallow than the bio-Technobabble.
 * There's no evidence that the ship was scrubbed in any way. Hell, judging by the interior of the ship, they were still pulling bits of the Normandy's old guts out and replacing them. And "individual biotic aura" makes even less sense considering what we know about biotics.
 * In fact, there's evidence for the ship not have been scrubbed (or completely taken apart, for that matter) at all, like the roaming space hamster and the lost ship models.
 * The whole point of Javik's ability is to give the Protheans an aura of mystery and otherness, and to demonstrate that there are still major holes in the current Cycle's understanding of the laws of the universe. Like with the "space magic" of the ending, you are supposed to get the feeling that there's still so many undiscovered things in the cosmos.
 * The Alliance only made sweeps for Cerberus bugs, as stated by Traynor. So, aside from retrofitting, there is no scrubbing otherwise.

The Lawson Family
Late in the game, we learn that Miranda and Oriana's father is a man named Henry Lawson. Now, while it's very strange to think Miranda would keep the surname of the father she despised it can, perhaps, be justified. But why on earth does Oriana, who was kidnapped as a baby, raised by foster/adoptive parents and then hidden from her father again carry the Lawson name?
 * You learn that information from your time during ME2 that Henry Lawson is Miranda's father. he engineered both Miranda and Oriana to carry his genetic legacy. Miranda kidnapped/saved Oriana and gave her to a nice family. Henry busted this during Miranda's loyalty mission in ME 2. The result should be that Oriana is saved and learns of her past and from then on keeps contact with Miranda. Reading your mail in ME 2, Oriana will thank you and ask that you watch over Miranda and even P.S.S. "Stop reading Sheperd's mail, Miranda." This would suggest that Oriana is also extremely intelligent and resourceful and could ahve known about her past all along. It could be inferred that since the ME 3 is through the eyes of Commander Sheperd, then Oriana would be known which is why her name is Lawson. Conversely, she has been found by Henry Lawson and so all illusion regarding her identity is broken.
 * You do not learn the name of Miranda and Oriana's father in ME2. Before the third game, the prevalent opinion was that Miranda would have chosen a new surname for herself, distinct from that of the father she despised. That this isn't the case is odd but not a huge problem. She may have kept it to spite him. The question is why Oriana would change her surname from that of the adoptive, loving parents who raised her to "Lawson" after learning her history. It makes absolutely no sense to me at all.

Terminal Ethnocentrism
Based on what we've seen, it seems clear that the Prothean beacons were designed by and for Javik's people, rather than some other Prothean race. They require you to think like a Prothean to get meaningful data out of one, can potentially kill someone without a sufficiently strong mind and are designed around Javik's race's inherent form of communication. Now that's all good and well if you're not planning on other species using them, but if the point was to warn the next cycle about the Reapers then why wouldn't they make their user interface a bit more generic? The one on Thessia was meant for the asari to use, but the asari don't have the Cipher—it takes the presence of Commander Shepard (or Javik) to activate the beacon. Javik's remark about "communication still being primitive in this cycle" seems especially narrow-minded since it presupposes that other races will have evolved his race's innate ability. The Protheans bet the future of all life on the galaxy on the hope that the next cycle would be just like them.
 * For all we know, Javik could be right. Evolution in the ME universe seems to follow some patterns (like different races developing the same Biotic powers, and the general similarities between races we're used to take for granted). For all we know, their "empathic" form of communication is going to show up in the future. The asari in special seem to be on their way to something like that, or at least similar. And they did manage to take information from that beacon (since it's the reason they're the most advanced race of the cycle), even if they never unlocked the VI, somehow.
 * Exactly. The asari already have, and probably had back then, moderate psychic ability, just ability limited to intimate physical contact and only practical use being Vulcan Mind Melds. The Protheans made the logical, if erroneous, assumption that this weak psychic ability would increase to the point of compatibility with Prothean Empathic Psychic Technology.
 * Implicitly the Prothean empathic abilities are something that can be taught or otherwise introduced to other species, since Javik appears to be mildly surprised that the "primitives" haven't mastered this skill yet, and since the Prothean Empire spanned numerous different species they all must have been granted this ability for Javik's surprise can make sense. Or perhaps they measured how "advanced" different species were on the basis of whether they shared this ability or not, and only conquered those that did.

Normandy's weapons
Several missions(the academy one comes to mind) involve the Normandy not being able to drop you closer or pick you up because a Cerberus ship is running interference. The Normandy still has those massive guns from Garrus' upgrade that tore through the collector ship like butter. Has Cerberus' tech upgrades gotten to the point that those aren't working anymore?
 * At Grissom, the Cerberus cruiser was right next to the Academy. I shouldn't need to explain what would happen if the Thanix was used on the cruiser in such close proximity to the station, considering what happened tot he last ship that they blew up with the Thanix.
 * Joker said that there were about a dozen fighters around the Academy. Far too many for the Normandy to destroy alone without taking severe damage or damaging the Academy itself. Even if they could, alerting Cerberus to their presence would jeopardize the lives of everyone on the station, making the rescue mission mute.
 * Let's not forget that Cerberus has copies of all your tech upgrades from ME2. So even if the Normandy has Silaris Armor, Cyclonic Barrier Technology, and a Thanix Cannon, so does that Cerberus cruiser... and its a little bigger than you.
 * Maybe. Just because they had access to the upgrades that you made doesn't mean they could apply them to every ship they own. Cerberus may have a mountain of cash, but those upgrades are expensive and applying them to dozens of ships may not be feasible. And the mission to the Cerberus base on Tuchanka would suggest that their ships weren't all upgraded: one good shot from the ground cannon tore the Cerberus cruiser apart.
 * Said ground cannon is also longer than a modern day aircraft carrier (and that's just the part we can see - it's likely partially underground), far longer than the Normandy. Even accounting for atmospheric slowdown on the projectile, it'd be a helluva lot more powerful than the piddly little gun on the Normandy, upgraded or not.
 * Not to mention that when you're an indoctrinated Reaper agent and the End of Days is nigh, you don't care about saving money for next year's budget. So yeah, shoot the wad, upgrade all your ships; go nuts -- you can't shoot credits at the Alliance.

Legion's Sacrifice
How come Legion still dies if you make peace between the quarians and geth? It babled something about "disseminating personality matrix" before dropping dead. Even if his physical body experienced terminal overclocking, shouldn't his programs be able to upload themselves away offsite, just fine? To me, it seems as if Bioware wanted to make it a Bittersweet Ending just 'cause.
 * It's because he was the only Geth left with the Reaper Code and there wasn't enough time for the average Geth to analyze and make it there own in time to help stop the Reapers, basically Legion had to be what amounts to an organ donor for them... that's my interpretation anyway.
 * In order to upload the Reaper code to the entire Consensus, Legion would need to disseminate every individual geth program in its body throughout the entire Consensus. It could not copy the Reaper code directly; the only way to spread the upgrades would be for individual programs to spread outward throughout the Consensus as a whole. The individual geth programs that made up Legion are likely still out there somewhere in the Consensus, but the personality that made up the discrete gestalt entity that was "Legion" is gone; the moment those geth departed Legion's platform, "Legion" ceased to exist - and because it made all geth truly self-aware, there's no way to reconstruct Legion.
 * In the end, Legion uploads the final Reaper code so that will enable all Geth entities to become self-aware. Since he cannot directly upload to the Geth consensus, he must transmit it via satellite at the cost of his personal entity. The final act of him referring to his body as "I" rather than "we" shows that the Legion persona made the sacrifice for all his fellow Geth. Sheperd even quizzically asks the Geth Prime if he is now Legion but the Prime corrects him and states that the one known as Legion has been terminated. Just like Morinth to Samara, you can copy the form but not the absolute personality.
 * That...Makes absolutely no sense given how computers work and how geth are said to work in the Mass Effect universe. The geth do not have blue boxes, they're just raw code. This is to say, assuming they are not philosophical zombies (beings that appear to be sentient but actually aren't), there's no reason just copying the reaper code wouldn't work. Or you know, just copying the necessary data from legion onto every geth...

The Crucible and the Conduit

 * Ok, many aspects of the ending give me a serious headache, but for now I'll stick to two major problems:
 * 1. Did the Reapers influence the design of the Conduit? I keep on getting confused whether or not that is the case. If they didn't, then why would the designers make things so damn complicated by making it activated by the Catalyst and thus make it have to merge with the Citadel? Unless I missed something...
 * Conduits are simply scaled down versions of mass relays, nothing more nothing less.
 * 2. Why would the Reapers build a Conduit ON EARTH leading directly to the Citadel? Why give the resistance's ground troops access to it? If it was so that the Reapers could send up their own troops to defend the Citadel, why does Shepard not encounter any resistance (not counting the Illusive Man) aboard the station at all? Unless either the Catalyst was somehow manipulating things or the Conduit just somehow formed on its own or moved to Earth from Ilos, it really doesn't make any sense (of course, it's definitely not unique in that sense).
 * Shepard and Anderson theorize in the game that the Conduit was used to transport humans to the Citadel for "processing", presumably to create a new Reaper. Using a Conduit is far more efficient than having to carry everything up via ship. The Reapers also had no reason to guard the interior of the Citadel simply because they never thought anybody would be able to reach it.

Reaper Strength
In Mass Effect 1, it took two whole fleets to destroy a single Reaper, and even then, it took outside intervention (destruction of Saren's Sovereign-possessed husk) to make it vulnerable. That same Reaper also had weapons in each of its tentacles. Yet in Mass Effect 3, the Reapers seemed to be much weaker. For one, they only had one laser, mounted on their undersides. For another, they are visibly taking damage and exploding during the final battle. Is the Worf Effect in play here, or was Sovereign simply unusually powerful for a Reaper?
 * I believe that one, yes, Sovereign was an abnormally strong Reaper, but two, there are a lot more ships being brought to bear in Mass Effect 3.
 * Also, keep in mind that weapons experienced some revolutionary advances after analyzing Nazara/Sovereign's corpse. Thanix cannons and all that.
 * The original battle scene is flat-out wrong. Bioware confirmed that the animators making that cutscene were not in active communication with the writers and portrayed Sovereign as simply being too powerful.
 * While it was the result of poor communication, there is nothing to indicate that the original scene is non-canonical. It can be easily explained by the fact that no dreadnoughts besides Destiny Ascension that was surprised pants down took part in the Citadel's battle, as well as the fact that Thanix cannons adapted from the Reaper tech have been widely adapted to large ships in the intervening years.
 * Sovereign is a Harbinger-level capital Reaper; the Reapers you're talking about are the relatively small Reaper Destroyers. Also, yes, Sovereign was very strong even for a Reaper; it's explicitly stated that three dreadnoughts equipped with futuristic reverse engineered geth and Reaper weaponry are able to kill one capital reaper.
 * Quite a few of the assets you find are research and intel relating to structural weaknesses in the reapers; way to bypass their defenses and counter their offense. This is info the fleets fighting Sovereign would have no way of knowing, where as Sovereign likely knew the full capabilities of all the ships mustered against it. Knowledge is power.

Earth Death Toll Numbers

 * Something that surprised me was just how (relatively) low the death toll numbers given for Earth seemed to be. In the trailer, we are given totals for the first day (2 million casualties) and first week (7 million casualties.) That tells us that Shepard has been out and about in the galaxy for at least a week. So let's say that is a good average for the Reapers (considering they got what amounts to a surprise attack and took out 2 million in the first day alone.) That means that Shepard would have to be out and about in the galaxy for 8-9 WEEKS just for the Reapers to match the total casualties that occurred during World War 2. (60 million estimated.) Not to mention the fact that Earth's population during the time of the games is at 11 billion while it was only 2.5 billion during the 1940s, so there are more than four times as many people around to kill. Granted, the Reapers wanted to capture and process humans to make the next generation of reapers, so it's possible they weren't doing as much damage as they otherwise could have. It's also likely that the numbers "Big Ben" gives in the trailer aren't completely accurate. But it still surprises me just how low those totals seem to be.
 * Like you said, they're trying to harvest humanity, not obliterate it. Emily Wong notes on her twitter that if they wanted humanity dead, they'd have just nuked everything.
 * True enough, but why not resort to their "nuking" strategy when they began to lose the battle for Palaven? While the Reapers were bringing Turians into their forces as Marauders, Harbinger says in the 2nd game that they are considered "too primitive" to be valuable to Reaper reproduction. It would have severely weakened the last stand on Earth had the Reapers simply decided taking Palaven was more trouble than it was worth and bombed it to hell and back. This seems to have been their strategy in the past against species they considered unfit, as all of the formerly-inhabited planet descriptions that mention "orbital bombardment" show.
 * The numbers in the trailer are most likely from London alone. As I recall, the Reaper harvester vessel can process 1.86 million individuals in a week, which would make for a good estimate if it was only a few weeks at this point. You shouldn't take Harbinger's words at face value concerning the turians either; they may be too primitive to make a capital ship, but they should still be good enough material for a destroyer, since those things are made out of "lesser" species according to the Codex. Personally I'm assuming that the Reapers bombard worlds from the orbit after the harvesting is complete to hide the traces of their involvement, not before when there's still material to be collected. Remember, the Reapers inevitably win any war of attrition, so they're not in a hurry. Time and indoctrination are on their side.
 * The Reapers were never "losing" the battle for Palaven. They were winning until the krogan intervened, but even then all they did was slow the Reapers down enough that the turians could devote resources to the assault on Earth.
 * Not really. The Turians and Reapers were more at a stalemate, as while the Reapers were there in force, the fleet sent was still not nearly as large as the bulk of the Reaper forces, concentrated on Earth. It's why Humanity's fleets, comparable in power to the Turians', were utterly obliterated(in the case of the Fourth and Second) or badly hit and damaged(Third, First, and Fifth). Plus, the krogans' entrance turned the tide to where the Turians were winning the battle. In terms of space superiority, the Turians and Reapers were also at a stalemate, as the Turians were definitely able to match the Reapers almost kill for kill considering that they had 56 dreadnoughts to Humanity's paltry 7.
 * Well winning/losing depends on how you gauge it. The Turians initial assault was really the most successful action against the Reapers by any single species (the Reapers lost two Capital ships in the first assault!) but they still lost the planet, the Reaper's were smart enough to realise that by rushing past and bombing/ground assaulting key areas on Palaven it made the battle in the sky virtually immaterial. A stalemate at this point is fine for the Reapers, they have access to the planet and the Turian supply lines, and the Turians can’t risk the full assault needed to dislodge them.

Missed a step, Doctor?
When Thane is fatally wounded by Kai-Leng, he stays alive long enough to be carted to the hospital and recieve rudimentary treatment. It couldn't save him, but it gave him time to say his goodbyes. However, his clothes in the hospital were still the one he'd gotten stabbed in. Did the staff remove his bloodstained and torn coat, perform surgery, and then put it back on later. It's not as if they don't use hospital gowns, since the Virmire suvivor recieves one and a human/asari gown would fit just fine. So, why not?
 * Unfortunately, all drell character models use the same clothes. (compare Kolyat, Feron, and Thane. Their outfits are of different colors but are essentially the same) Bioware probably just didn't choose to give Thane a unique character model for the hospital.
 * He was brought to emergency surgery immediately after the stabbing. As I understand, in those circumstances hospital gowns are a waste of time; just cut off whatever is in the way and get to work.

Have to space it?
If you betray Wrex, he comes at you with a shotgun but ultimately ends up getting shot to death through a window. Bailey comments that Wrex may be too big for a coffin and they'd have to space him. Why? The Citadel has Krogan passing through there fairly often, and Elcor, which are bigger than Krogan, are Citadel members. Surely they'd have those guys die every so often. Do both Krogan and Elcor not have a tradition of burial?
 * In case you didn't notice, the Citadel is kind of at war. Resources in general are going to be limited, and the amount of coffins the Citadel would have in stock for krogan would be limited too. Even less if krogan troops are moving off of Tuchanka and fighting the Reapers.

Tarquin Victus big screw-up
What, exactly, was Tarquin Victus major screw-up that he is repeatedly accused of by his soldiers and your squad members? As far as I can tell, he was faced with two equally bad alternatives: Attack a dug-in enemy head-on and suffer guaranteed casualties OR try a risky approach which has at least some chance of surprising the enemy troops at the price of high vulnerability before the landing. I just don't see how he is supposed to have screwed up for chosing caution over suicide. The only reason I can think of is that he acted against the Turians main strategy to attack the enemy head-on with overwhelming force, or am I missing something here?
 * It was less that he made a bad call so much as he made a call that got his team epically massacred. Any commander who makes a decision that gets virtually the entire unit wiped out (especially if it goes against standing doctrine) will get in deep shit.
 * Especially if they fail to complete the mission to boot. With the "Victory at any cost" mentality of the turians, if Victus had managed to complete his mission at the expense of most of his team there would probably have been no complaints, but they got colossally screwed before even getting close to their target.

Tali and spiders
How does Tali even know what a spider is? Has she encountered some on the Citadel? On Omega? In human colonies?
 * Rachni + Extranet.
 * Apparently multiple planets have animal species that can be described as "fish" (IE, "Thessian Sunfish"). I wouldn't be surprised if there were eight limbed arthropods on other planets... or she could have just future-googled "spider".
 * Tali clearly knows what an insect is (otherwise she wouldn't be able to say Rannoch has no insects), it's no stretch to think she knows what a spider is. Also, even though Rannoch has no insects, it's interesting to note that Tali never visited Rannoch in her life. For all we know, insects are a very common concern of the Quarians as they are today, specially considering they usually buy used ships.
 * Any translator can tell you that there are words or concepts that can't be fully translated into other languages and must be approximated. When human talk about "spiders", Tali would hear it as her word for whatever species approximate spiders in her homeworld. Even if there is no such species, a good Universal Translator would readily give an approximate definition easily understood in her language. So, there will be no difficulty in understanding what a "spider" is.
 * A better question would be why people in-game keep comparing the rachni to spiders. The queen did look kind of spiderish, but in the first game she and all of her children looked very much like giant space prawns. If anything, they should be crustaceans, not arachnids (and yes, I did notice the arachnid/rachni thing).
 * Simple. Tali does a Wiki Walk on the extranet, ends up following a link to Earth Spiders, and what she reads (or sees videos on) freaks her out. Bam, arachnophobia.

Piloting a Geth Ship
After the Geth Dreadnought mission, Legion pilots a Geth fighter to get Shepard and his two squadmates back to the Normandy. It does so by having its mobile platform physically operate the controls, just like any organic would. Why the heck are Geth ships built with this kind of controls? A race composed of software processes would have a much better response time if they cut the mechanical middle-man, and simply uploaded themselves into the ship. The same goes for the many terminals found throughout the dreadnought.
 * The geth seem to have deliberately designed themselves to operate like organics. Maybe as an effort to understand individual organics or individuality, or maybe they just felt like doing things physically, with a mechanical body, instead of operating via software. Note that when interfacing with any geth technology, you see lines of light running between the geth's fingers and whatever they're doing, so it is probable that the geth is likely just directly interfacing with the equipment directly while in a mechanical body. Geth may also limit their pilots to single mechanical body to cut down on reaction time; imagine, if you will, over a thousand individuals trying to pilot a single fighter while in contact with another five million other individuals controlling a fleet, all of them of the same rank, and all of them operating under the basic idea of reaching a consensus on what to do. Even arguing at the speed of optical processor thought, they're going to take a while to make a decision. A dozen geth isolated in a single body, however, can make decisions instantly and quickly.
 * While the first part might be true (even then, trying to understand organics by seriously handicapping themselves in a life-or-death situation is kind of stupid), the second part makes no sense. Even with the mobile platforms physically interacting with the ships, we still have the same amount of Geth programs running and trying to reach a consensus during a fight. The mobile units just add a bigger delay between reaching the consensus and acting on it as the mechanical components take more time to transmit the information (and that's what operating any machine is, transmitting the information of what you want it to do by pressing buttons/pushing levers/etc.) than a software does.
 * Incorrect. Legion points out that while geth are contained inside mobile platforms, they do not have as direct communication with the Consensus. Data is transferred, but the amount of communication is stifled. It is "quieter." Imagine being in a room with twenty million other soldiers all of the same rank trying to figure out what to do with everything at the same time and reaching a consensus on how to do that. Legion itself took thirty minutes to come to a conclusion with only a thousand geth debating, and that decision was a stalemate. Now imagine the aformentioned twenty million peple trying to decide on every movement of every ship in the entire fleet plus their support craft. It would be insanity. Dividing up individual functions to individual platforms allows those geth to efficiently perform their specific task while directives are passed back and forth. Instead of twenty million geth trying to come to a consensus on fleet acrions across the entire fleet, you have mere thousands, hundreds, or dozens operating individual functions and communicating those back and forth. Data transferrence remains, but individual decisionmaking at each task becomes more efficient. Instead of twenty million geth making the decision on where to move every fighter, you have a few million deciding general course of action and instantly passing that down to other geth servers controlling ships, which transfer refined directives to individual stations, which transfer further directives to platforms handling specific tasks, on down the line, at light speed. Individual platforms at individual stations can quickly react to changinging circumstances without having to wait for the primary Consensus to reach a decision. Not too dissimilar from how human navies operate, except communication is almost instantaneous.
 * It still makes little sense for a geth fighter to be piloted by a foot-soldier platform when it could just as easily be a platform itself. In ME1 we're told that their "tanks" (armatures and colossi) are platforms unto themselves, rather than vehicles driven by a foot-soldier platform, precisely because that's more efficient. If they were preoccupied with operating more '"like organics"' that wouldn't be the case.

Ruined Suit, Perfect Face
When Harbinger shows up before the conduit and blasts the entire ground force apart, Shepard takes a direct hit reflected in his/her damaged armor. But how the hell is his/her pretty face just fine afterwards, even if you weren't wearing a helmet? Hell, Shepard's armor melted off the tough bastard, and there's not even burn marks or lacerations or anything. It's not as if it can't be rendered (think Virmine Survivor in hospital, bloody face during opening), so what caused Bioware to overlook that?~
 * I guess it's a case of Gameplay and Story Segregation (or, more to the point, "Presentation and Story Segregation"). They just didn't want Shepard to look any different from their regular self during the final sequences, so they just added some of the Renegade scars to their face and called it a day.
 * My Shepard was pretty noticably scarred in that scene, especially around her mouth.
 * While you'd expect considerably more damage to the face, we don't really see Shepard survive a "direct hit". Harbinger's laser strikes the ground in front of her, the force of which is enough to obliterate her armour and blast her back. Well, okay, she's actually much closer to the beam when she wakes up. Lots of speculation for everyone.
 * That's easy. Shepard, like all people in the Mass Effect universe, wears a helmet in combat, which you can turn off in the options for the sake of Gameplay and Story Segregation, because people want to emotionally connect with him/her which isn't possible if you can't see his/her face well. When he/she was hit by the beam, the helmet's outer layers melted just as much as his/her armor, making them opaque. Because he/she didn't want to walk around blind, he/she 'actually' pulled off her helmet, revealing his/her bruised but unburnt face.

Banshees
Why are they roughly 7½ feet tall when asari are all generally the same height as human women, other huskified species mirror their organic counterparts in size (yes, brutes are significantly larger than krogan, but that's attributable to visible cybernetics)? The codex says Banshees disintegrate immediately upon being killed. This occurs every time the player takes one down. So why is Falere able to point to the corpse of one during the Ardat-Yakshi mission?
 * The Reapers are physically modifying the bodies with massive amounts of cybernetic augmentations.
 * Likely either a one-in-a-million design flaw, or the Codex's definition of "immediately" doesn't equate to "instantly". On the note of Brutes though, their anatomy and articulation don't look anything like a krogan's. Hell, it looks more like a Yahg's. Even the feet resemble them. What's up with that?
 * It also resembles Turian feet. I think Brutes are not just mutated Krogans with Turian heads, but a complete mix-and-match of the two, with the end result resembling neither.
 * The mission makes it clear that transformation into a Banshee is not instantaneous, it could be that it was killed shortly before the transformation was complete and so the insta-disintegration wasn't working yet.

Indoctrinated Access to Vendetta (Thessia Beacon)
How was Kai Leng able to download the data from the beacon on Thessia? When he arrives, the VI notes that "an indoctrinated presence has been detected". Given that Shepard and Co. had to convince it to give them information on the Catalyst, why doesn't it shut down or otherwise refuse to give Leng the data?
 * The VI is just a highly advanced operating system, isn't it? It's not too hard of a stretch to think the information it protects can be hacked by other means. Besides, it doesn't give Leng the data so much as Leng "kidnaps" it. The data is retrieved by others at Cerberus at Chronos station. More surprising is that Leng is able to transfer the entire contents of a Prothean beacon into his omni-tool.
 * Not so surprising if his omni-tool was designed/upgraded with downloading a Prothean beacon in mind. We know that Leng knew what he was looking for on Thessia; it's a fair assumption that TIM armed him with the tools he would need to get the job done, as opposed to sending him in blind and hoping for the best. As for why Vendetta told them about the Catalyst, a simple answer is "He didn't". Vendetta is a program. A Prothean program, which may or may not be far more advanced than anything that modern galactic civilization has, but is undoubtedly inferior to the Reaper tech that TIM has at his disposal. They probably just stripped all the data they needed from him without giving him a choice.

Fleets getting through the relay

 * According to the Codex, the Migrant fleet takes days to get through a relay. Now, presumably, the Earth Battle sees a good portion of that fleet (under best conditions) as well as thousands of ships by other races. How come they are all "accounted for and ready" within a minute?
 * The Migrant Fleet tends to be cautious, and the more ships you send through, the further the error ratio when they exit. You can send a giant fleet through the relay, but it will be scattered, but the Migrant Fleet does not like to move while spread out. They move through a few ships at a time to make sure that none of them get separated and grabbed by pirates. Sword Fleet doesn't have to worry about that, so they can send hundreds of ships through at once without immediate worry; by the time the Reapers can respond, they'll have already reformed.

Air Car Brakes

 * Why, oh harsh and uncaring gods of Cutscene Incompetence, could I not just simply slam on the brakes and send the ridiculous idiot trying to stab my Citadel aircar to death flying out over my windshield and down to his messy death?
 * Cybernetic legs with magnetic feet?
 * They still pass pretty close to a couple walkways, if they just flew up a little bit they could knock him off pretty easily still.
 * That's really easier said than done, and fiction blows up how easy it is to do this. You ever actually flown a plane before? And have you ever had need to scrape something off the top of said plane by ramming it against an object overhead? No? because they don't train you in doing that, and they don't train people flying planes to thread things that closely. All that's likely to happen if you were to attempt that would be the abrupt, crunching end to your flight career - and that's without factoring in that Kai Leng isn't going to just sit there and let Shepard try it.
 * Its not so much that I believe it would be easy as its something I believe Commander Shepard would do or at least try to do. Its not the fact that it doesnt work so much as the fact they dont try because frankly it just makes sense for Shepard (especially survivor Shepard) to be at least know a few more ways to get something off your car.
 * Why not just stop under one of those overhangs and then go straight up? Kai Leng has two choices; jump off or get smushed. And since you're not trying to do it at high speed, the worst you'll do is dent your roof. Of course, he might try to hang down and attack through the window, but I'm pretty sure he can't dodge bullets -- or biotics, or tech powers -- while hanging by one hand in front of a car window.
 * Stopping in place would just invite Kai Leng to stab Shepard in the face thanks to the suddenly very stable platform he's got and the perfect opening it would give him. Even then, accelerating straight up runs into the complication that about a tenth of a second after Kai Leng hits, Shepard will also hit.
 * Its kinda hard to stab Shepard 'directly in the face' when you're standing on the back half of the car, and Shepard's in the driver's seat.
 * No. But by that point Leng's already achieved his objective in disabling the car anyway, so it doesn't matter. If Shepard tried to ascend at any point prior, Leng could have simply stabbed Shepard while he was on the front of the car.
 * Actually, on rewatching the scene, he could have done that anyway. Shepard never jinks the car while he's standing on the front of it; nothing stops him from just killing Shepard instead of the aircar except the fact that its not in the script. Which brings us right back to the original objection of the entire aircar sequence being horribly scripted; it makes both Shepard and Kai Leng look like total idiots.
 * Pretty much. They're the same thing that keeps Shepard anchored to the deck in all those zero-gravity sequences, and ubiquitous enough that Shepard would know there's no point. The mere fact that Kai Leng is even able to stay on the car while its moving at such high speeds indicates that he's using magnetic boots.
 * Except that he's freely walking around on top of the car, indicating that whatever magnets he's using they are able to be overcome by the leg strength of a cybernetic leg. The momentum of a human-sized mass (his own) being decelerated from 150+ mph to zero in several seconds would be many many times that amount of force. tldr; Short of his actually welding himself to the car, even magnetic boots shouldn't have been able to hold him on during a crash stop.
 * No. Magnetic boots would be reasonably expected to have variable grip strength, especially if they're part of the cybernetics Kai Leng has equipped, and if they're part of his cybernetics, they would be able to recognize the difference between a sudden unintended acceleration/deceleration and a nerve impulse ordering the leg to move and thus triggering a detachment. They'd be fairly useless if sudden acceleration or deceleration threw their wearer off, considering how often such devices would be used in zero gravity and the potentials for sudden acceleration/deceleration in such an environment.
 * Um, what? Magnetic boots are used for keeping yourself in place on exterior hulls while going EVA. EVA operations occur in places like space stations, dry dock, and ships drifting in orbit. They are not intended for standing outside on the hulls of units undergoing high-G maneuvers. Hell, remember the whole firefight you had with the geth and the krogan on the outside of the Praesidium tower during the end of ME1? How much impact did it take you to knock their magnetic boots free of the station and send them helplessly flying away up into zero gee? Not much. And you can't say that geth wouldn't also have their magnetic boots 'spliced directly into their nerve impulses', seeing as how they're entirely synthetic.
 * Magnetic boots are used for keeping yourself in place on exterior hulls while going EVA. EVA operations occur in places like space stations, dry dock, and ships drifting in orbit. They are not intended for standing outside on the hulls of units undergoing high-G maneuvers. And this precludes them from being strong enough to keep their operators from being throw off said objects in a catastrophic situation....how, exactly? Its reasonable to assume that magnetic boots would be designed to anchor in case of a serious emergency.
 * Hell, remember the whole firefight you had with the geth and the krogan on the outside of the Praesidium tower during the end of ME1? How much impact did it take you to knock their magnetic boots free of the station and send them helplessly flying away up into zero gee? Not much. And you can't say that geth wouldn't also have their magnetic boots 'spliced directly into their nerve impulses', seeing as how they're entirely synthetic. If the geth didn't feel the need to anchor their disposable platforms onto surfaces sufficiently to withstand powerful biotic strikes, that's their perogative. One force's inability to properly equip their troops does not translate to every force's equipment, especially considering that this is Kai Leng, the most important Cerberus operative in their entire organization. The fact that he seems perfectly willing to drop down onto a moving aircar and has no trouble moving around on it indicates that he's confident that he can survive any high-speed maneuvers.
 * "The no limits fallacy is the illogical idea that a poorly understood phenomenon can be extrapolated to infinity or assumed to not have any maximum value or threshold." You can consider this line item to be the rebuttal to both arguments above.
 * So you're not actually going to bother arguing at all or even saying anything about how said fallacy relates to my point? Thank you, concession accepted.
 * What part of 'your entire argument relies on the baseless assumption that magnetic boots have no upper strength limit' did you need explained to you? Electromagnets require power. The man isn't walking around with a 10-gigawatt mass effect core shoved up his ass. There are stark engineering limits as to how strong his magnetic boots can be, and its nowhere near as strong as the amount of momentum an entire aircar engine can deliver, unless you want to get into fantasy-land of assuming that Cerberus can fit something more powerful than an aircar engine into a cyberleg.
 * It gets worse. When Kai Leng lands on your aircar, he's originally standing on the windshield. Magnetic boots don't stick to glass.
 * For the same reason you are lasering things into piles of goo and splatting the heads of enemies with your $200,000 sniper a moment before, then the cutscene starts and you pull out some piece-of-crap pistol and miss every shot. The plot needs him to survive.
 * The simplest explanation: Shepard tries to shoot Leng because Shepard never took the "What to do when a ninja cyborg jumps onto your aircar" class at N7 training camp. S/he sees a threat dropping onto the aircar, and the immediate ingrained response s/he possesses is to go for his/her gun, not jam the brakes or swerve the car or try to scrape the threat off. S/he also doesn't have the advantage of sitting safely behind a keyboard and being able to stop and think for hours on end as to what the proper tactical decision is. Shepard sees Leng, and his/her first instinct is to shoot the threat dead, not maneuver the vehicle to throw the threat off.
 * Yeah... except that 'just hit the brakes!' was literally my first reaction on seeing the scene, as it was happening. If my couch-potato ass can think of this virtually in real time, somebody with Shepard's reflexes should have thought of it before Kai Leng's feet even hit the car.
 * Just because that was your instant, Genre Savvy reaction to it does not necessarily mean that it was Shepard's immediate reaction. "Draw weapon and shoot target" is going to be Shepard's first response to a threat like that. Again, you're sitting safely behind a TV screen with a controller on a couch. Shepard is there, in the middle of the situation, and has to make reflexive, snap decisions; his/her snap decision at that point was to draw a weapon and engage, not abruptly reduce forward thrust. The latter has an outcome that would likely be better, but Shepard simply didn't think of it.

Haestrom

 * So, was there any explanation as to what was happening on Haestrom in ME 2? It was one of the non-missable recruitment missions, and the game went out of its way to note that the sun was aging too fast and no one had any explanation. It seems like there's still a loaded Chekhov's Bazooka sitting on the mantelpiece here.
 * That's a direct result of Karpyshyn leaving the development team. See Aborted Arc on the main page. The galaxy being on the verge of destruction by dark energy was the original motivation for the Reapers.
 * Just be happy that they scrapped that. It would have pretty much required the destruction of all mass effect technology to achieve a happy ending. Hopefully some DLC or sequel will eventually make something out of Haestrom with appropriate retcons, though.
 * Many fans think that would have been a vastly superior reason than the explanation we got.
 * Many fans think anything would be better than what we got. Don't get me wrong, I'm as disappointed with the ending/s as the next guy, I've ranted about them, picked out the plot holes, the whole nine yards. That being said, the dark energy ending, from what is known about it, sounds even worse. For all the unanswered questions the current ending left us with, the DE ending only leaves us with more. How, exactly, is fusing advanced species into sentient starships supposed to stop the spread of dark energy? If mass effect technology is the cause of the spread, then the reapers opposing it makes no sense as they are the source of the most advanced mass effect technology in the galaxy; the relays, the citadel, and themselves. By making more reapers with more powerful mass effect cores, they're making the problem worse. Also, and this is going back to the first question of how they got from "Step one: make reapers" to "Step three: save galaxy(aka profit)"; what does the genetic diversity of a species have to do with the result? But all of this is trivial compared to the biggest point of all; the complaint about the endings as they stand is that your actions throughout the game don't matter; you're given a(blue), b(red, and c(green). The only difference the dark energy plot offers is that it takes away one of those choices. You'd be given a(become a reaper) and b(don't become a reaper).
 * That was inherently the point, as per Karpyshyn's style. The Reapers would have been likely blind to themselves being the biggest cause, or aware they are and use it as an excuse. Mass Effect 2 hints that the right kind of supernova makes eezo, *cough* dark energy/matter buildup *cough* so it could be in the Reapers' best interent to let it happen so they can get more of their fuel. The notes that were leaked were hardly the whole story, and given how many things ME 2 pointed out and kind of made you notice, like ME 1 before it, there was a lot of things that would have contributed and probably answered things in that original story. QED; ME 1 points out a planet with a huge scar that could only be caused by a massive mass accellerator, and lo and behold, you find the target of that exact weapon, the Derelict Reaper in ME 2. From an innocuous but interesting tidbit to sizeable plotpoint is how Mass Effect did it, minor red herrings nonwithstanding.

Liara's pre final battle Asari merger "gift"

 * When you talk to liara on earth right before the final battle she will offer a gift to shepard. I couldn't even understand how she tried to describe it, and if you accept, then the screen will go black and you and liara will watch some kind of weird space event in total silence (and making out, if you romanced her). What the hell was that supposed to be?
 * As I recall, she pretty explicitly states that she's going to share some of her memories with you. Presumably, the white light that engulfs them is supposed to represent a number of her experiences being shown to/shared with Shepard. We aren't given more details than that, but I don't think we really need them either to understand the idea.

Liara and the Shadow Broker

 * So if you don't do that Lair of the Shadow Broker DLC, it's revealed that Liara still overpowered the Shadow Broker. How? She just hired a bunch of mercenaries. How does this make any sense at all? The Shadow Broker has a galaxy wide criminal empire with tens of thousands of agents, and has been in the business for decades. He has enough resources to change the course of galactic politics, control entire planets behind the shadows, and deploy hundreds of soldiers on a minutes notice. Liara has absolutely no experience and has only been a local information Broker on Illium for two years. How did she even survive Vasir's assassination attempts (Vasir had an army with her, remember), let alone hire enough mercenaries to overwhelm the Shadow Broker, who should have a whole lot more resources than her?
 * My guess is that Vasir got cocky and underestimated Liara. With Commander Shepard there she had her guard up and had her army there in order to deal with Shepard, not Liara. She probably got the drop on Vasir and took her out, then with the clout that she killed a Spectre hired her own small army to deal with the Shadow Broker. And let's be honest here, it's more realistic that a highly trained mercenary group would succeed in taking out the Shadow Broker than 3 people in a frontal assault.
 * And remember that Feron dies in the 'you didn't help Liara' path; it took Liara a lot longer to gather her mercenaries and put together her assault, apparently. And the Shadow Broker's ship wasn't really that massively guarded -- it didn't have any antiaircraft guns, for example. Its main protection was secrecy. Once you've gotten past that, its just a matter of killing a platoon of heavily-armed security guys and then taking down a bigass yahg with a machine gun. In other words, within the competence range of an experienced mercenary unit.
 * Liara's own rebuilt defenses were also overrun pretty easily by Cerberus when they moved against her, to the point that she only escaped by ramming their ship with her own while she snuck out on a shuttle. Liara will even point out that the ship's only real defense was secrecy if you ask her what happened.

Blood Pack
In Aria's mission, you assassinate the Blood Pack leader and replace him with one loyal to Aria; problem being, both leaders are vorcha, where as ME 2 made it clear that the vorcha had no authority in the Blood Pack, and were just cannon fodder for the krogan bosses. Did Shepard whip out every krogan in the blood pack in 2(hyperbole)? While we're on the subject; the Blue Suns leader; I'm playing on an import where Vito survived Zieed's misison; how did he lose control of the Blue Suns?
 * In Mordin's loyalty mission, you kill the current leader of the Blood Pack. Presumably there were some changes in the way the group was run during the six month gap between 2 and 3. As for Vido, there's a bit in the leaked script which didn't make it into the final game where Zaeed reveals that he assembled a team to go after Vido, but the Reapers got there first. Zaeed saw Vido getting carried off by a Harvester. Vido begged for a Mercy Kill. Zaeed decided that Vido didn't deserve one and walked away. That being said, since that wasn't in the final product, it's probably non-canon.

Why don't you just shoot him?
To be clear, I know the narrative reason this didn't happen, I just can't think of a logical in-universe one; during Thane's fight with Leng, Leng is knocked prone for several seconds by Thane's biotic PAWNCH. I assume the reason Thane didn't press the attack is that he was out of breath from the exertion and needed a second to recover. My question is why the hell didn't Shepard start unloading on Leng while he was on the ground? During the fight, he didn't have a shot because of Thane and Leng tussling, plus he and his squad had to secure the councilor. But really, your squadmates could handle securing the councilor while Shepard backs up Thane, and while Leng is on the ground, Shepard has a clear shot; Thane's not in the way, he's off to the side out of Shepard's line of sight, and there are several feet between him and the target. Not to mention, Shepard is an extremely good shot. Leng should have been swiss cheese at this point.
 * Cutscene Incompetence, which appears in spades whenever Leng does. It's also possible (though not stated) that Shepard wanted him alive to interrogate later.
 * Simple. The blue and (sometimes purple) bar that appears over the name of just about everyone you shoot at in all three game. Shields kind of negate your options to quickly kill somebody; in the time it would have taken Shepard to even meaningfully deplete Kai Leng's shields, he would have been back up on his feet and engaging Thane again, and by the time he'd get another shot off the shields would have regenerated.

Dead Reapers(some ending spoilers)
Why don't the Reapers take better care to collect their dead? We know of at least two that were just left where they lay(the derelict reaper and the leviathan of dis), and given how old those two are, it's obvious that reapers have been getting killed during the harvests for a while. Thing is, these aren't just troops or war assets; these are living museum pieces. The whole point of harvesting is preserving species in reaper form; these reapers may no longer be awake, but they're still active in some form, and represent the continuity of species extinct for tens/hundreds of millions of years; don't the reapers place any value on that?
 * I think the Reapers are suffering from a severe case of Believing Their Own Lies.
 * Or they think "Meh, maybe that species wasn't worth it after all."
 * They may have simply failed to locate them. The Reapers aren't perfect and the galaxy is big.
 * To quote [[http://masseffect.wikia.com/wiki/Harbinger_
 * Bear in mind that a dead Reaper is still a powerful weapon, capable of indoctrinating those who stray near it. One of the reasons why the Batarians fall so easily is because a dead Reaper indoctrinated several officials who went on to sabotage their infrastructure.

Reaper Reproduction
How many reapers do the reapers make from a single harvested species? The games seem to imply one species= one reaper, but this seems horribly inefficient to me. Now, my estimates could be wrong, but based on sheer biomass, 11billion humans should be more than enough to make multiple capitol ships. Also, assuming it is one species, one reaper, the reapers should ultimately lose any war of attrition; maybe not in a single cycle or even a dozen, but sooner or later their numbers should dwindle. If it's one for one, then in this cycle they're only getting one(possibly two, we don't know what the battarians are being made into) capitol ship/s and at most, twelve destroyers. That seems a fair bit shy of the casualties they've taken this time around.
 * We don't have hard numbers on how many organics it takes to produce a single Reaper, or even if they only produce one Reaper per species. Saying that they only produce one Reaper per species is baseless.
 * Also remember that this cycle is not typical. The previous cycle managed to sabotage the Citadel to prevent the Reapers from using it to divide and conquer. They may only have lost a handful of capital ships in all the previous wars.

The quarians and the Treaty of Farixen
After Admiral Shala'Raan admits that many quarian ships are technically dreadnoughts, then Shepard has the option of chewing them out for breaking the Treaty of Farixen and Shala'Raan accepts that they broke it (although somewhat flippantly). Why? The quarians are not a Council race and the Treaty is between Council races only, so the quarians are not actually subject to the treaty.
 * The Migrant Fleet's status as part of the Citadel sits in a gray area. They frequently pass through Citadel territory and do deal with the Citadel, i.e. when they were trying to claim a particular planet in Citadel space for a colony. So they apparently do fall under Citadel jurisdiction, at least while in Citadel territory, and are bound by their restrictions, including Firaxen.

Shepard can't hold his/her liquor?
In Mass Effect 2 it takes three shots of the green stuff, one shot of batarian ale and one shot of ryncol to drop him/her. S/he also managed to survive deliberate poisoning from the batarian bartender on Omega. In Mass Effect 3 it only takes three shots to make Shep fall asleep on the couch. I know it's the end of life as we know it and people will be drinking pretty heavily, but are they really just slinging out shots of krogan liquor to the average patron? Or is Shepard just getting old?
 * Maybe it's dextro-based?
 * Could be. We see one of the bartenders dancing instead of serving drinks so it could be their minds aren't on the job. Still, that seems like a pretty big mistake to make and the kind of thing you'd want the new hires to know from Day 1. Wouldn't you make sure the bottles are color coded so you don't accidentally poison your customers by giving them the wrong kind of drink? Three times in a row in Shepard's case, no less.

Fall of Thessia

 * Why does everyone instantly act, following the end of the Thessia mission, that the entire world is dead and gone? Fighting was still going on on both Earth and Palvan when the same happened to them, and I get they have bigger militaries, but resistance was still happening on Thessia. It ain't dead, just something more to fight for. In between Liara's (understandable) grief of Thessia being taken over, she seems to conveniently forget that both Palaven and Earth have had the exact same thing happen to them, and both Shep and Garrus are upset but resolved to fight for it. Neither seem to think to say "Uhh, I can actually relate. Notice how I'm focused on how to kick their ass off my home planet?"
 * Because the Asari were considered to be the most widely respected and powerful species in the galaxy, the first ones since the Protheans to achieve interstellar flight, the first to discover and inhabit the Citadel, the list goes on. Them not only losing a planet to the Reapers, but their home world no less, would've been a huge morale hit for everybody.
 * Thessia has no unified resistance like on Earth or Palaven. The lack of unifying central authority that made the asari unusually liberal, accomodating and creative in peacetime has the downside that prevents them from having a way to coordinate a unified military effort in war. They have the best individual fighers in the galaxy, but those have little use against giant deathmachines of doom, and their dreadnoughts are tied in the Citadel fleet. In result, Thessia is way worse off than either Earth or Palaven, both which are on the brink of a total military defeat by the end of the game, as well. As for Liara's reaction, her personality is very different from either Shepard or Garrus. She has no military training, and has far harder time to separate her personal feelings from the fight at hand. Hence, her reaction is much stronger than either of the two when she sees her own homeworld burning. Not to mention that the asari aren't nearly as good with dealing with sudden, unexpected changes as humans or turians are, due to their long lifespans and static culture.
 * Because the planet is dead and gone. Thessia has minimal military forces and no heavy ground forces, and there's no krogan army to support them. The turians on Palaven survived as long as they did because every city on the planet is a fortress and they're ridiculously militarized. Human forces on Earth survived as long as they did through raw tenacity, and even then the damage was catastrophic. Thessia's military is simply too limited and too focused on commando units engaging in attacks against an enemy that fights conventionally instead of how the Reapers operate. Meaningful resistance is wiped out almost immediately.
 * Believe it or not, Thessia did better than most of the other planets the Reapers hit. Take a closer look at the codex entries and the other wiki: the Reapers basically had to resort to using siege tactics on the asari because they couldn't harvest a planet populated by five-and-a-half BILLION biotics using brute strength alone. Considering that Thessia was one of the last planets to be invaded before the Reapers were defeated, my guess is they got off rather lightly.
 * Even so, I agree. Dakuuna was overrun so badly the planet had to be completely evacuated. Earth has been burning since the war started. Thessia being taken by the Reapers doesn't mean the asari aren't surviving somehow or that they can't stall until help arrives. I also found it weird that because the Reapers took the planet everybody was so stunned and shaken. Speaking critically, having the Reapers take the Citadel would have been more emotionally powerful.
 * It's not just that Thessia itself was lost, it's that Kai Leng made off with the Prothean VI they needed for the Crucible. Not only was Thessia fucked, but the rest of the galaxy looked that way too.

Cerberus working with the Collectors?
Vega says his squad was killed because of a "Cerberus spy, working WITH the Collectors". How and why in the hell would Cerberus be working with the Collectors? Why would Cerberus work to sabotage the defense of a human colony when their whole objective in ME 2 was to prevent the abductions?
 * Vega is not omniscient. You're currently fighting a Reaper-allied Cerberus, so he may have made the connection there. Or he could just be flat-out wrong.
 * The true goal of Cerberus was not to prevent the abductions, but learn as much about the Collectors, and by extension the Reapers as possible. It was strongly implied that the Illusive Man leaked Virmire Survivor's presence on the Horizon to the Collectors to cause the attack. In the loosest sense of the word, Cerberus was indeed working with the Collectors for a bit, albeit with the intention of destroying them and stealing their technology.

The Reapers haven't watched The Terminator
Ok, by now we all know the reapers' plan. What I see as the biggest flaw in the Catalyst's logic is that it makes the assumption that organic life will conquer ftl travel sooner than it will develop artificial intelligence. Now, assuming this was to happen and the worst case scenario were to occur with the A.I. killing the pre-spaceflight organics that created it, would it not be possible if not probable for the A.I. to become itself spacefaring and potentially cause the destruction of galactic life halfway between reaper harvesting?
 * Presumably the Reapers kill off any synthetic races they find during their harvesting runs. At most, the pre-FTL synthetics would go undetected during the current cycle and then be wiped out 50,000 years later.
 * The Reaper vanguard's job is to make sure this doesn't happen. It keeps an eye on the galactic situation, and if a synthetic creation starts running amok, it would trigger the harvest early to deal with it. This is a common fallacy that a lot of people make when considering the Reaper's cycle: they assume that the Reapers are blind to the goings-on of the galaxy, when the Reapers have both their vanguard (Sovereign) and slave species (Collectors, controlled by Harbinger) to keep an eye on the galaxy for precisely this reason. Remember that the current cycle is an extreme fluke because Sovereign couldn't just call down the Reaper fleets early. In previous cycles the Reapers would just swoop down on any abnormalities and smash them flat.
 * That is flat-out wrong. Javic says that the Protheans were engaged in a galactic-scale war with a Synthetic species for much of their history, and were starting to make real gains when the Reapers came.
 * Which proves what, exactly? The Protheans were fighting a synthetic species, yes, but that synthetic species was not on the verge of winning and taking over the galaxy. The Reapers would be expected to trigger a harvest if it became apparent that synthetic life was going to take over the galaxy; that's the vanguard's job.
 * Moreover, as long as the Synthetic and Organic species are fighting themselves to a standstill, that just makes the Reapers' job easier. Once one of them seizes the upper-hand decisively, they can move in an smash both of them at their weakest.
 * The problem is that according to the Catalyst Synthetics always win.
 * So? The Catalyst is not a truly omnicscient and infalliable entity. The fact that you're talking to it proves that much outright.

Salarian contribution to the war assets
If you choose to sabotage the genophage cure, the only exclusive reward that you receive is the Salarian First Fleet war asset, which is worth 150 points in military strength. If Wrex is alive, you will be sacrificing a total of 405 points from the Krogans (30 from Wrex, 300 from Clan Urdnot, and 75 from the Krogan Mercenaries) in exchange for token Salarian support. This totally removes the entire supposed moral dilemma of pragmatism vs. idealism and instead, making anyone that actually sabotage the genophage cure into Stupid Evil territory. Also, the Dalatrass promised you that the Salarian Union will provide the Alliance with both full military support and their best scientists to work on the Crucible project, yet said scientists never shows up in your war assets.
 * It doesn't change the moral dilemma, it shows that there are consequences for your actions. Note that if Wreav was the clan leader you still keep all the krogan support and get the salarians.
 * The reason it undermines the choice, though, is because it goes from "doing what's fair vs. doing what will be best for everybody" into "doing what's fair and best for everybody vs. fucking things up for everyone".
 * From what perspective? You only know that you will lose all krogan support much later on; at the time you make the decision, Shepard believes it possible to secure krogan support and salarian support. Don't come to fallacious conclusions when you have the advantage of hindsight.
 * Nope. You can get almost full krogan support, if you killed Wrex on Virmire and made sure that Maelon's research was destroyed. Wreav will still promise full krogan support, and you'll take a small hit from Baraka dying, but Mordin and Wreav still being alive make sup for those hits. The moral here is to be consistent. You get more resources being a full Paragon or full Renegade than you get for waffling between them.
 * If Wreav is in charge of the Krogan and Bakara is dead, that changes things entirely. Wreav is likely to start another galactic war with the renewed Krogan population, which makes Dalatross' sabotage pragmatic while hoping that Wreav will keep things under control and curing the genophage is right is idealistic.
 * Even if Eve survives, so long as Wreav is in charge you can still get Krogan support while sabotaging the genophage. You also get a bonus from Eve, although in that case Mordin will die whatever you choose. Also, this isn't really a Paragon vs Renegade thing - Wrex could be saved through either means (letting him die is more a "didn't bother upgrading Charm or Intimidate" solution than anything else), and saving Maelon's data is considered the Renegade choice.
 * (The OP) Another thing that bugs me is why does salarians support worth so little towards the war effort. Out of all the major galactic powers, they are the ones who's home world hasn't been overrun by the Reapers yet and their territory is relatively untouched by the war yet (except for the Cerberus raid on the STG lab). Meaning that their industrial complex is still intact and functional, but the maximum possible asset points that you can get from them is 363 (Kirrahe+First Fleet+Third Fleet+ Mordin+ STG). On the other hand, the krogans lack any form of central military command or recognized government, not to mention not even having a navy. And their economic and industrial power is almost non-existent. Yet Clan Urdnot alone is worth more then the entire salarians fleet combined. Are the krogans just that powerful, or are the salarians holding out on you and not contributing fully to the war effort?
 * The Alliance News Network entries note that the salarians are more interested in self-defense than assisting other species, and that some of the more powerful salarian families are threatening outright secession if significant resources are pulled away from defense. So yes, the salarians are not able to fully commit their forces to the war effort at Earth. that and the krogan are just that much of a powerful ground force that they can add that much weight to your war effort; the only other force in the setting that can even come close to providing such a powerful ground element are the geth, and even they are lagging behind the krogan.
 * What isn't made entirely clear in the game is that different assets have value asigned differently based on how they're deployed. Krogan assets are ground forces and make up the bulk of that; they're value is assigned vs reaper ground forces, not the reapers as a whole. Ships and fleets have value asigned based on how they stack up to the reapers themselves. Total assets are divided into three groups; ground forces make up the Hammer strike team. Fleets and ships make up Sword and Shield fleets. Hammer stands alone, Sword and Shield work together. The krogan are so valuable because they are the most effective infantry in the galaxy; all your other ground forces combined don't add up to the total the krogan bring to the table.
 * What further unbalances it is that all of your krogan assets go towards Hammer ground forces and in fact make up the bulk of Hammer. The salarian fleet would go towards the combined Sword & Shield space forces, and considering that you more than make up for that with a dozen other fleets, it's really not that big of a loss.
 * War assets don't matter with regards to whether it is a space element or a fleet element. They both add to your overall forces. Ground elements speed up the advance on the surface so that fleet elements don't suffer as much damage; fleet elements can hold space for longer, giving ground elements more time to advance toward the target point. Both support one another in the overall objective.
 * Salarian military might is in intelligence. However, I like to think that the assets you gain are the ones that Shepard can personally call upon. There are dozens or hundreds of fleets and armies, but they're out fighting the war proper, not unlike the characters from multiplayer (only the promoted count toward Shepard's assets).
 * There's actually a hint towards this back when you pick up Eve. If you talk to Kirrahe before going in, he will flat-out tell you that the STG (the only real significant Salarian force) is behind you no matter what some politician decides. Frankly, the moral question is unaffected by the reward: it's still about saving the Krogan vs. protecting the rest of the galaxy from the Krogan, and her offer is the character, not the game itself, trying to sway you to her side.
 * In one of the conversations with Admiral Hackett, he essentially tells you the same thing.

Asari ignorance and the beacon
In Priority:Thessia it's revealed the Asari have been in the possession of a fully functional Prothean beacon for the last 50,000 years. In Mass Effect 1, even a broken Prothean beacon is able to transmit enough information to make the existence of the Reapers immediately known to Shepard, even before he got the Cipher. So even without any further action, anyone who came close to the statue of Athame would have had visions of the Reapers and have been utterly convinced of their existence. So why didn't the Asari do anything? Hell, even if you argued that the beacon didn't send out those signals because it worked too well, they should still have gone after the Cipher for the same reason they're stated to have kept the beacon hidden: to aid their own development.

Another matter of less importance is who are said to be involved. The Asari councillor says that only higher functionaries in the Asari government know, but the Asari work through a direct e-democracy without representatives except a handful in the Citadel Council for interspecies affairs. How would politicians manage to constantly leak revolutionary technology without anybody finding out, when they don't even have the authority to distribute scientific funds? Then it becomes even worse: Liara says Matriarch Benezia was also involved in the conspiracy, but she's got nothing to do with any formal position in Asari government, she's just an Asari with a lot of private power and wealth, and her status as Matriarch is granted because of her age. The entire conspiracy plot reveal just makes no sense.
 * While we aren't explained the matter very well, we can assume that this beacon for one reason or another did not transmit the signal as intended, and only the presence of a living Prothean could activate it, and the asari would not know about the Cipher that would allow them to simulate this eventuality. It could simply be damaged; 50,000 years is a long time, after all. As such, they only managed to extract small amounts of data and study the structure of the object itself to give them an edge in their technological development. As for the political angle, in the asari culture Matriarchs are highly respected, and while their society practices direct democracy, most citizens in practice defer to the decisions of Matriarchs who are known for their wise decisions. As such, there would still be unofficial concentrations of power in the hands of relatively small cliques of Matriarchs on Thessia. And if you read and listen about Benezia enough, you'd know that she is one of the most powerful and influential Matriarchs in the galaxy, a major player in business and politics, as well as a religious authority. It makes perfect sense for her to be a part of the coverup.
 * Also, we don't know the rate of advances the asari had pre-spaceflight. They are pretty smart, so it's reasonable to say that they were careful when releasing technology the beacon helped produce. Besides, just like in our world, the fake researches could be attributed to rich, individual funders. As for the "why they didn't do anything", well... there are many paranoids about the end of the world around here. They say they have evidence, but most people think they're crazy. Asari government is not based on centralized power, so it could be even more difficult to convince people that the blurry visions are not a misinterpretation of something else. Liara even said that few people still believe in Athame anyway, maybe for the same reason many religions today are bashed: Because their message is just not understood/"true" for the people.

Just use Lift on him
Anyone Genre Savvy knew that Lieutenant Victus was going to die disarming the bomb, but the way they did it left a big gaping hole in logic. As far as drama goes it was a good cutscene, really played up the whole Redemption Equals Death and Heroic Sacrifice tropes, but a few hours later I realized that it didn't make sense. Hey Shepard: when the bomb detonator is falling and Victus is going to be squashed by several tons of metal, why don't you call one your biotic teammates to grab him with a mass effect field and pull him to safety? You can't even argue a Gameplay and Story Segregation here, because biotic powers are a main part of the universe and are frequently used in cutscenes.

Yeah, there would be a problem if you didn't have a biotic squadmate on that mission, but hell, Bioware did something similar in Dragon Age II: if you don't have Anders with you and you take your brother or sister into the darkspawn caverns, they invariably die. If they really definitely wanted Victus to die, they could have just changed the scenario to make his death less preventable.
 * Realistically, in the time it would take Shepard to call a biotic teammate to grab Victus, he would have already fallen to his death. Shepard might be able to grab Victus, but there's also the question of just how much good simply grabbing him in a mass effect field would do. It would likely simply drag him to the side for a couple of seconds, then release him, and he'd fall to his death anyway.
 * You forget the power Pull, which brings the target towards the caster, and lasts long enough that it would have gotten him to safety.
 * Not necessarily. Pull drags the target in the direction that it hits the target. With Victus falling, the Pull it going to hit from above and pull him up, but isn't guaranteed to carry him all the way to safety before it releases him. Most pulls only last for a few seconds as well. Not to mention that Victus' armor likely has shields, and the Pull won't work through them.
 * Shepard and his squad are still fighting Cerberus anyway.
 * Shepard is actually watching Victus for about ten seconds before he pulls the final machine piece out and falls. Granted, that's not enough time to call his squadmates over, so it would only work if Shepard was a biotic.

Thane's Final Moments
Not sure if it was just my playthrough, or if it's been actually fixed yet, but during Thane's final moments in the hospital is something of a wallbanger, at least when I got to it. When you go to read from the book with Kolyat, and Thane turns to face the window before he dies, he was clearly still breathing through the entire scene. Just that little glitch, which makes Bioware seem a little absent minded about a supposedly emotional scene, makes it all hard to connect with anymore. I mean, he's likely not wanting to face the two when he actually dies, but with him continuing to breath it actually looks like he's just getting more comfortable to rest...then they essentially assume He's Dead Jim, while he continues to breath even as Shepard leaves.
 * Terminally ill or critially wounded people rarely just die and go still; the usually slide into a coma from which they don't wake up again.
 * Ever personally witness it? It really is unrealistic sometimes, but Thane's problem WAS breathing, and any major damage would severely inhibit him ability to do anything, particularily that. Hell, it was outright stated that Thane could die from strenuous activity, nevermind being run through. In any case, read the scene, the scene is played as him drawing his last breath with them in the room. It's easily assumed that's why Shepard closes Thane's eyes before he leaves, and the animation continuing hurts the scene's impact.
 * I was more bothered by the fact that his eyes were still clearly moving under his eyelids even after he died.
 * His eyes weren't even closed in my playthrough.