Mass Effect (video game)/Headscratchers/Archive 1

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Evidence Against Saren

 * So, you walk into the council with this quarian technology expert who no one's ever met before. She plays a static-y snippet of someone who sounds kinda like Saren saying something conveniently incriminating (notice the only fragment she claims to have is the most damning one), which she claims she got from the memory core of some random geth. And the Council go "This evidence is irrefutable!". WHY?!
 * Wouldn't you trust a quarian to know about the geth?
 * Audio recordings just like this are permissible in modern courts, so long as they pass authentication. If the information was taken directly from a geth memory core, presumably it would have telltale markers, just like how real audio recordings can be authenticated. The Council probably authenticated the information before reviewing it, and would have run audio tests against samples of Saren's own voice to make sure it was his voice, which is another thing that can easily be done using modern technology. And Tali never says that's the only piece of information she has, just the most relevant.
 * Its also worth noting that Tali had assassins after her for this information as well. That's a rather interesting piece of correlating evidence.
 * Not to mention Garrus' own testimony is available on how Fist was working to have Tali killed on Saren's orders, further corroborating that she had some genuine goods on Saren.
 * Plus they could easily get further information to corroborate the data as well; Doctor Michel, for example, and information from the bodies of the men who tried to threaten/kill her, possibly information acquired by Jenna while she was working in Chora's Den, etc. There's also direct hard information available from Fist's own bar, possibly the recording of the conversation with Fist where he talks about Tali, Tali's own testimony....hell, if need be, the Council could even go to the Shadow Broker for further evidence, as the Shadow Broker did hire Wrex to kill Fist because Fist betrayed Tali (and the Shadow Broker) to Saren.
 * I have to agree with the top-level poster. I don't think Tali being a quarian means anything. Any race could have that clip for whatever reason. Also, I'm not sure how they could run tests to authenticate it if they were hearing it for the first time there, which seems likely, considering she was made to actually play it. If it was given to them in advance they wouldn't require Tali playing it before they claimed it was the evidence they needed. They couldn't do any analysis on it without having the sound available for playback, either. I also don't think any witnesses would matter, given how they already discarded someone else's testimony against Saren. Having Fist's people after her didn't mean much, either, because whether her evidence was real or fake, it was just as damning, so he'd be just as likely to try to have her killed if he knew she had a fake audio clip of that sort.
 * Then the Council (and you) have to ask yourself this: Why would Saren want to kill some random quarian who claims to have evidence about him being a traitor? The humans are one thing, after all Saren could, and did, say that it was just Anderson trying to ruin his reputation by saying "Anderson is just mad because he washed out of Spectre training and blames me." Tali is fresh from the Flotilla, she had never met Saren OR anyone in the Systems Alliance. She would have no reason to "frame" Saren. Wrex and Garrus, especially C-Sec officer Garrus, would have added their testimonies to the report; Wrex was to kill Fist for betraying the Shadow Broker (who the Council would have to know about) because he was trying to either kill Tali or turn her over to Saren and Garrus, as an officer, would testify about Fist's men trying to coerce the Doctor into giving up Tali's location. Why would a random krogan, a random quarian, and a cop lie about a rouge Spectre?
 * "I don't think Tali being a quarian means anything. Any race could have that clip for whatever reason." Being quarian establishes credibility and familiarity with the geth, which is important, as the recording was taken from a geth.
 * "Also, I'm not sure how they could run tests to authenticate it if they were hearing it for the first time there, which seems likely, considering she was made to actually play it. If it was given to them in advance they wouldn't require Tali playing it before they claimed it was the evidence they needed." Except Tali isn't playing it directly for the Council. Ambassador Udina takes it to the Council personally. There's an implied period of time that passed between Udina getting the recording and Udina presenting it to the Council, which is all the time that is needed to authenticate. And the Council wouldn't be convening at the drop of a hat because Udina comes running back into the room an hour later; it would have taken time to establish another hearing. Logically speaking, the second Council meeting had to have come at least a day later, probably setting up both Saren's guilt and Shepard's promotion well before the actual "televised" Council meeting. In fact, the first ME novel makes it explicit that the Council generally tends to make decisions well before a particular meeting is called.
 * "I also don't think any witnesses would matter, given how they already discarded someone else's testimony against Saren." They dismissed a statement by a single panicked dockworker who overheard a name being spoken. That's a far different matter when compared with multiple corroborating testimonies from reliable sources, including a C-Sec officer.
 * "Having Fist's people after her didn't mean much, either, because whether her evidence was real or fake, it was just as damning, so he'd be just as likely to try to have her killed if he knew she had a fake audio clip of that sort." Except if the evidence was fake, that would have come up during authentication tests. Regardless of whether the information was real or not, the fact that he tried to have her killed is, at the very least, going to raise eyebrows. A Spectre ordering a random person executed for any reason is going to make C-Sec at least start looking into it, especially as Executor Pallin has a raging hate-on for the Spectres.
 * Bit late to the party, but I'd like to note that Pallin doesn't doubt Saren's guilt. Ask him about Saren before it's proven, he'll say something to the effect of "Saren's bad, we both know that."
 * Believing that Saren goes a little overboard in pursuit of a mission is a long way from "Saren is working with the geth to destroy all of civilization."
 * Maybe, but Saren's had a number of atrocities on his record that the Council has swept under the rug or pretended to not notice to keep from losing face. Now that he's been proven to have lied about being on a human colony attacked by geth at a very questionable time, the Council has no choice but to cut him off since it's proven that Saren is no longer controllable. They still don't believe that he was an envoy of the Reapers ( as of ME 2, they still don't want to believe in the Reapers at all), but they'll act since the potential problem is too big to ignore. They are politicians, after all.
 * If you bring both Tali and Wrex with you onto the elevator leading to the Council chamber before presenting the evidence, Tali will point out that the Council wouldn't have accepted the evidence if it were only presented by "a lone quarian with no credentials." Clearly, the evidence being presented by Shepard and Udina, without Anderson "tainting" the evidence, and coupled with all the other violence and additional evidence they could present, probably tipped things in their favor.


 * Okay so the Council doubts your claims in regards to Saren and the Reapers due to your evidence being questionable. So why doesn't the asari Council member simply use her mind powers to discover something? Liara, being "only" 106 years old can do it...So why couldn't a Council Member do it?
 * Liara was looking for very specific material only she could interpret and understand, and that takes two beacons and the Cipher to provide. The asari Councilor would have no idea what to look for or how relevant the information is, and even Shepard's memories themselves are questionable - Sovereign's conversation could very easily be dismissed as a highly sophisticated VI. Or dismissed as Saren yanking your chain with a "Max Headroom" utility relaying you his words dubbed into a synthesized voice and scary image.
 * Not to mention the looking into someones mind is a very emotionally personal thing, and the fact the Liara did it was to get information during a desperate situation makes sense, where Councilors would never be that personal with some random Spectre.
 * This fails the sanity check. If the survival of every sentient being in the galaxy is at stake, the asari are pragmatic enough that they wouldn't refuse just because "it wouldn't be proper". Even if the Councilor didn't do it herself, she could have a trusted agent do it. The previous point still stands, however.
 * Saren being a hologram at the time might have had something to do with it.


 * Why in a futuristic world was there no camera to capture a video or image of Saren on Eden Prime? Don't say it's because the video/image could be faked, because the Council accepted a third party audio recording.
 * Presumably, Saren simply didn't appear long enough to be caught on camera, and no one was around to capture him on camera anyway, after the geth slaughtered everyone. The geth probably also destroyed any evidence they could that Saren was present, and were in the process of making sure of it when you arrive. Cole himself was just a dock worker, and he'd have no reason to have a camera on him, and even if he did, wouldn't likely have the presence of mind to use it, and there's no evidence Nihlus had any kind of recording equipment on hand either. And as far as is indicated, Saren only showed himself at the docks and possibly the excavation site, and that was after the geth killed everyone they could find. No one was around to record him, and it was only dumb luck that Cole saw his meeting with Nihlus.
 * It is reasonable to presume that Spectres, being elite espionage agents who are also military special forces, carry helmet recorders and such along with them much like UNSC marines in Halo. It's also reasonable to presume that Saren, an experienced Spectre himself, would a) know exactly where a Spectre like Nihlus generally keeps his mission data recorder and what it looks like and b) remember to loot it off the body before he left.
 * Or perhaps Eden Prime just doesn't have enough of a crime problem to warrant the cost of surveillance cameras.
 * Also, one of the civilians tells you that the mysterious geth ship is pumping out hellish soundwaves, and Shepard says that it's probably to jam all communications.
 * It seems almost certain that the noises they were hearing were actually Sovereign's indoctrination field, though.
 * It can be both. An indoctrination field that can also block communications and mess up ground-side cameras.

"Shepard: "Saren is allied with the geth! He's using geth technology!"
 * Shepard accuses Saren of collaboration with the geth. The Council dismisses these charges, claiming insufficient evidence. I assume none of them notice the prosthetic geth arm prominently grafted onto Saren? Or the glowing blue circuitry in his face? And it's no use claiming the prosthetic arm may be simply that - the art book specifies that it is in fact a geth arm and that its sole purpose is to show just how deeply Saren is in it with the geth. Why not just give him the arm after his Council hearing?
 * Holographic transmission technology seems quite sketchy, so no one could see he had implants at the hearing, and it's never stated Saren set foot on the Citadel after he got the arm. If someone asked a question, he could have easily just dismissed it as a fancy piece of armor and/or cybernetic implants he had created for him or something, especially considering the level of resources he has access to.
 * Also, Shepard isn't accusing Saren of associating with the geth; s/he is accusing him of attacking the Eden Prime colony. Any evidence of contact with the geth is just circumstantial evidence, and he would no more be guilty of Eden Prime's attack than someone associating with the batarians would be guilty of the attacks on Mindior or Elysium.
 * Well, not really. The batarians are a varied race, and there are several decent individuals amongst them. The geth on the hand are a race of robots who have done nothing but kill any organic life that gets in their way, and they show zero individuality, especially since their intelligence is very limited. They're not even sapient on their own. So anybody who is allied with the geth is at least very suspicious.
 * Well.. the geth are sapient and sentient individually. They're just more so in a group. And considering the first act they witnessed as an uplifted race is their creators trying to commit genocide on them... they're probably not exactly going to willing to talk to non-organics. Note that if not for Saren approaching them, they would have stayed in the Veil for the foreseeable future and Tali and Shepard mention how the geth revere the Reapers. Robots yes. Mindless drones... not so much.
 * Even so, its not like Shepard can prove its an arm of geth manufacture, when Saren isn't even available in person, and Shepard doesn't even know the arm is of geth design in the first place. Unless Shepherd has the magical power to tell what species manufactured a device s/he'd never seen before and has had limited prior contact with their technology, and that consisted of mostly destroying said technology instead of analyzing its pleasing aesthetic design. And if Shepard did magically manage to figure out that the blocky, transparent shape in the hologram of a person s/he's never seen before bears some vague resemblance to the aesthetic design of the machines who'd s/he has spent most of his/her time blowing to pieces, the accusation would probably play out something like:

Saren: "What? Ridiculous. This is a custom made piece of technology I had developed by one of the many, many arms manufacturing companies I have perfectly legal investments in. Can we get back to real evidence now? Like the human's mystical dreams being used as evidence against me?""


 * Actually, eff the Council - Why the hell didn't Nihlus notice or even pass comment on Saren's physical changes when he was standing less than three feet away? "Oh, hello Saren my old chum, that's a nice prosthetic arm and geth-like bionics you have implanted there, I'm sure you didn't have them the last time we met. How about them geth, huh? I'll just turn my back to you and ponder their presence while ignoring the fact that you appear to resemble this particular type of synthetic. By the way, since subtlety is not known to be your strong point, how did you manage to sneak by all these ge-" * BLAM*
 * Bigger problems at the time. Nihlus is surprised that Saren's there, but the geth are the bigger problem ATM.
 * Also, we can't be sure when the last time Nihlus saw Saren so Nihlus not knowing about the prosthetic can't be established. Or how long Saren has had it. We also don't know about the state of amputations in the ME universe. It may not be as unusual a sight as we're shown. Also, bare in mind the typical turian attitude as noted in the Codex; Saren basically lied to Nihlus asking him a question who would have assumed a basically truthful answer especially from a friend he's known.
 * I think I read somewhere that the cyborg Saren we see was actually supposed to appear much later in the game, perhaps not until the final confrontation where he explicitly refers to Sovereign giving him 'enhancements'. Until that point they were going to have a non-cyborg Saren model, but it was cut. I assume they used the cyborg model because it's just more interesting and more evil. This would also cover Nihlus's failure to mention the implants at the beginning, since they would not have wanted to re-record dialogue by the point they were having to cut content.


 * Alright, maybe someone out there can follow this: On Eden Prime a shot is fired, which prompts a giant squidship to take off and one frightened dock worker to tell Shepard what they saw. While its not exactly firsthand evidence and the guy has no idea of the power structure in play, its a good lead. Later on, Anderson gives his take on Saren that comes across as a little opinionated. At this point, the character hasn't had a bit of personal experience with Saren. The report makes sense, the Council is understandably skeptical of their top agent, Saren is understandably defensive, and Shepard is understandably yelling at everyone like Saren just shot his dog-- wait, what? Where's the strong reaction coming from, given that everything up to now has effectively been hearsay? Why won't Shepard let me leave maturely? It just bugs me.
 * See it from Shepard's point of view. Hundreds of colonists and marines died on Eden Prime, including Jenkins, a member of their crew. The horrific images of the Prothean Beacon have been burned into their mind, such terrible things that haunt even a hardened marine. S/he has an eyewitness account of what happened, including a name - what, did Powell just make it up on the spot? And their mentor, a respected soldier and war hero, has told them just who Saren is, and it fits perfectly with what's happened. Shepard's pissed, and he's got a target for that anger. It makes a lot of sense.
 * YMMV then. I came into it expecting Shepard to be something more of a voiced, customizable AFGNCAAP, and felt that the game was railroading me unnecessarily.
 * I'm really irritated that Shepard can't keep his/her cool, even if they're really pissed off. S/he keeps it together in pretty much every other situation where s/he's making a committed effort to persuade people of things.

The Ending

 * Even if the Council dies, wouldn't the respective species appoint new council members? How could humanity take over the Citadel unopposed?
 * By having physical possession of Citadel Station, which is invulnerable to conventional assault and the central control node for the mass relay network. You can hold all of galactic civilization hostage if you own that thing. Note that Sovereign was able to successfully attack Citadel Station only by both having a) vastly superior technology and b) root user access to Citadel Station's defense systems.
 * Plus a big honking fleet of geth to back it up. Even then it was a tough fight.
 * Presumably, if the Council was destroyed they would have also lost a lot of the support staff and government officials, either in the geth attack itself or on the Destiny Ascension. The Citadel government would be in complete shambles and the center of their seat of power would be under the control of a human fleet that would not have suffered heavy losses saving the Council, while the cream of the Citadel fleet, including the most powerful dreadnought of their entire navy, would have been destroyed fighting the geth. The double whammy of losing both a huge part of their fleet and their entire government would give the humans plenty of room to move in and take over.
 * The problem is that the Treaty of Farixen makes the Alliance Navy a lot smaller then either the turian or asari fleets and everyone got the crap beaten out of them at the Citadel. Humanity would control the mass relays but they are needed for communication as well as transportation. After humanity pulls off their power grab, what is to stop the rest of the galaxy from finding out when a relay to Earth is open, jumping a fleet there and telling us to "give up the Citadel or we'll turn your home planet into molten rock"? All in all it seems like a very bad idea to try to grab power from more powerful and established races.
 * Keep in mind, humanity is the ones with the keys to the Endofthe World As We Know It.
 * It's implied that the Council fleets took extremely severe casualties in the fight with Sovereign, and that by appearing at the last minute the Human fleet did not. With their remaining force dispersed throughout the galaxy and no Mass Relay access to allow them to link up, the alien fleets could be picked off at will.
 * Also, the Treaty of Firaxen doesn't make the Alliance fleet smaller; it simply limits the number of dreadnoughts the Alliance can deploy. They can build as many cruisers and carriers as they like, and can mob enemy dreadnoughts with fighters.
 * Plus, the Council fleets are going to be out and about securing Citadel Space from all manner of other troubles, i.e. the Terminus Systems. They might not have the manpower to dislodge the humans if they take over, especially in the resulting confusion of the destruction of the entire Council and if the humans are running the show well enough.
 * "After humanity pulls off their power grab, what is to stop the rest of the galaxy from finding out when a relay to earth is open, jumping a fleet there and telling us to "give up the Citadel or we'll turn your home planet into molten rock"?" The massive Alliance fleet sitting at Arcturus Station for one thing.
 * From the in game codex: "Systems Alliance: Military Doctrine:" The Alliance military is of great concern to the rest of the galaxy. At first contact with the turians, they were completely inexperienced. turian disdain changed to respect after the relief of Shanxi, where the humans surprised them with novel technologies and tactics. The human devotion to understanding and adapting to modern space warfare stunned the Council races. For hundreds of years, they had lived behind secure walls of long proven technologies and tactics. The Council regards the Alliance as a 'sleeping giant'." The codex also goes on to say that humans invented carriers, so even though it may be smaller, it's much more threatening. It is reasonable to assume that the various races which are admittedly "afraid of humans" would rather surrender. For minor races like the elcor and volus, it'd just be more of the same anyway.
 * Speaking of which, it wouldn't be difficult at all for the humans to establish a significant power base by allying themselves with a bunch of minor races. Remember how peeved the volus ambassador was that his species had never been offered a seat on the Council even though they'd been on the Citadel longer than most if not all the other minor races? Well if the volus feel like they're getting the short end of the stick, chances are some of the other minor races do too. If the humans promised to give these minor races greater influence in Citadel policy in exchange for their support, the Systems Alliance could create a coalition powerful enough to rival or even surpass the combined might of the Big Three.
 * The humans, even though they have a smaller fleet, seem to be the only race to understand the concept of "guerrilla warfare." (Again, it says so in the Codex.) Plus, canon clearly states that there were more turian casualties in the First Contact War than Human.
 * Uh, no? The asari and salarians' methods of war are also explicitly stated to be guerrilla in nature.
 * Also, if the Council is killed, the Destiny Ascension is also destroyed in the process; the reason this is important is that the DA literally carries more firepower than the rest of the asari fleet combined. Effectively speaking, by letting the Ascension get destroyed, Shepard just about instantly hamstrings one third of the Citadel's primary military force.
 * Either way, it kind of becomes irrelevant; Mass Effect: Ascension indicates that the canonical end for the game was the Paragon choice, where humanity saved the Council.
 * Not at all. Mass Effect: Ascension was vague enough that both the Paragon and the Renegade choices were equally appropriate. What the novel does point out, however, is that the species will eventually grow resentful of humanity for their newly elevated status.
 * Actually, Ascension specifically states that a human representative is being considered for the new seat on the Council; as the Renegade ending has the Council wiped out and humanity taking over in the resulting power vacuum, that would indicate the Council survived.
 * It also says one of the Council seats as well. The author even outright stated that you could just insert your own personal version of the events from the first game.
 * It bugs me that people always automatically assume that Paragon ending = Council survived and Renegade ending = Council dead. It's possible to play a mix of Paragon and Renegade, y'know.
 * It's entirely possible to play as a near enough pure Renegade without being a bigot. Which means you can refuse to save the current Council on purely tactical reasoning (i.e. not wasting resources saving what amounts to figureheads) and then appoint a new Galactic Council of asari, turians and salerians complete with a new seat for the Human Councilor.
 * Don't forget that even with the Council dead, humanity still has the reputation "Saviors of the Galaxy." Even if that reputation would wear thin over time, at least at first, that gives you a heckuva boost in the PR department.
 * That's an euphemism, seriously I hope there will be at least a Church for revering Shepard in Mass Effect 2 or something on that magnitude.
 * Who knows, we could very well have a fringe sect venerating Shepard. Its happened before.....


 * Why is it that it's up to you to decide whether the Council lives or dies? Shouldn't Admiral Hackett make that call since he's the highest ranking officer?
 * Point. Perhaps Hackett is just trusting your judgment, considering you're the guy/gal who's been dealing with the situation from day one (OK, even so, the guy in the spaceship with the scanners who's also an aged, experienced Admiral should still be calling the shots, but that's all I got).
 * The man in the field overrides the man in the rear. Hackett is trusting you to make the right call, especially when dealing with an enemy that the Alliance has no experience fighting. Because let's face it, you're the only person who knows how to defeat Sovereign and the geth.
 * Compress: Hackett lets you make the decision because Sovereign is a literal Giant Space Flea From Nowhere - you're the only person in the galaxy who has any knowledge of it whatsoever.
 * There's also that if Admiral Hackett happened to have a different idea from you, exactly how on Earth can he enforce it? Not only are you not legally subject to his orders, you're the guy with his hands on Citadel Station's master control panel while he's stuck light-years away on the other side of a mass relay that won't even work for him until you decide to unlock it.
 * To boot, you're also in the middle of battle while Hackett doesn't know what's going on. He's trusting you to make sure that you don't send the Alliance Fleet right in battle... right in front of Sovereign or some other bad situation.

The Destiny Ascension and Citadel Fleet

 * It's bigged up in the beginning as being basically the biggest and most kick-ass ship evaaar. When the ending comes around and it's got to USE those huge guns it sits there and does NOTHING except EXPLODE unless you tell the Alliance's lesser ships to babysit it. Yes, it is but one ship, but we never see it fire its much-hyped gun. Should I just blame the cutscene animators for this failure of the law of conservation of detail?
 * The gun isn't meant to be used at close range.
 * Someone Did Not Read The Codex on space combat. The DA is a dreadnought; dreadnoughts are built for massive, long-ranged combat where they maneuver to get their main guns to blast targets tens of thousands of kilometers away. One of the major strategies in space combat is to maneuver the ships inside the firing arcs of the enemy ships' main guns - essentially getting them in close enough that they can move faster than the enemy ship can pivot to target it with their main guns. The battle at the Citadel was a close-relay "knife fight". The geth fleet got in too close for the DA to use its main gun, so it was forced to rely on broadside mass accelerators and GARDIAN lasers, and was overwhelmed. This is explained very clearly in the Codex, and the battle is perfectly consistent with how close space combat is described in the codex.
 * This implies that the asari built an Awesome but Impractical ship. The general idea behind dreadnought-class ships, according to the Codex, is that they require frigates, and other smaller ships, to keep the enemy at bay so they can use the main guns of theirs, inflicting the massive damage they are capable of. The turian fleet certainly didn't do its job in that respect.
 * I think that the turians actually did their job pretty well, they just got overwhelmed by the sheer number of geth ships they had to fight. Plus, they were focusing on Sovereign, as it was the greatest threat, but Sovereign did a pretty impressive job soaking up the damage.
 * Plus Sovereign just steam rolled the entire defending fleet. They put a wall of ships and Sovereign literally rammed them out of the way. They didn't even slow him down. With Sovereign tanking the entire Citadel fleet, and the geth already being fairly close as is, the geth were able to quickly get to knife-fight range, and the Citadel Fleet mostly consisted of the Destiny Ascension and turian ships. The Codex also mentions that the turians have the most Dreadnoughts of anyone, so it's not impractical to think that a lot of the turian ships were Dreadnoughts as well. Not to mention that Sovereign himself has a LOT of powerful guns, and since he tanked up to close range, he could have reasonably blown away many of the frigates and cruisers with his own guns, leaving the Dreadnoughts to be whittled down and eventually destroyed by the geth.
 * Let's also not forget that Sovereign and the geth fleet essentially dropped in out of nowhere through the Conduit. It's not entirely unreasonable to surmise that by the time they had actually dropped out of FTL speeds (which the Codex clearly states makes it impossible to track a ship), they were already underneath the effective range of the Destiny Ascension's main guns.
 * Nitpick, but the fleet didn't use the Conduit, only Saren did with a foot army of geth. The Conduit is the small relay inside the Presidium that you go through in the Mako. Sovereign used the regular mass relay system.


 * The armada at the Citadel is Awesome but Impractical. It consists of dozens of cruisers and a lead dreadnought, all of which are fairly useless as the mass relay is pretty much right next to the Citadel and well inside their ideal range. Since the geth seemed to be fielding overwhelming numbers of close range frigates they were able to dominate the fight, especially since as mentioned everyone focused their fire on the Nigh Invulnerable Sovereign. It's likely that no one ever considered the possibility than anyone would be brave enough to actually attack the Citadel, especially since by their intelligence no one bar the established Citadel races would stand a chance against the inevitable counter attack.
 * Not that impractical. Note the length of time that the battle lasts; it takes Sovereign quite a bit of time to get from the relay to the Citadel, appearing to be about ten to fifteen minutes. Assuming Sovereign made a massive beeline straight for the Citadel, without slowing down, the relays were likely a fair distance away from the Citadel itself, more than far enough for the main guns on the dreads and cruisers to cut in and blow any normal fleet to pieces.
 * I disagree. There is no reason for the Reapers to place a relay such a distance away from the Citadel. It is likely far enough away to prevent chaos in traffic, but not far enough away to waste time. Although, while the game only shows one mass relay in the Serpent Nebula, the codex explicitly states relays orbit the Citadel (because it is the hub of the galaxy). There is no telling which one Sovereign's fleet came through (or if he was smart, his fleet came through them all... at the same time).
 * That does not change the fact that it takes Sovereign between ten to fifteen minutes to get from the relay to the Citadel. In terms of transit time, it isn't that long or far when transporting cargo/passengers, but it is a fair distance in tactical terms, and it makes sense to have the relays that far out if you're making the Citadel into a fortress, to give the defenders enough time to close the arms. The Citadel looks fairly close in stellar terms when Sovereign and Co. drop out of the relay,, but that's probably a trick of perception and size, as it still takes them a while to get there.
 * First: Why is Sovereign taking 10-15 minutes to get to the Citadel from the relay a "fact?" I don't recall a timer during the sequence. I honestly don't see 15 minutes going by in that span. Please, point out how that much time goes by. Second: The Citadel was not built to be a fortress. It was built to look like a fortress to give the defenders a false sense of security when the Reapers show up to devour them. The Citadel was made to provide a central hub the primary race in the galaxy can use to centralize their dominance, making themselves easy pickings for the Reapers. Once the Citadel trap is activated, all the Mass relays in the galaxy are turned off to be reactivated by the Reapers at their leisure. This is so the Reapers can take their time with what they are doing, and no communication goes out. This being known to us, along with the fact that the Citadel's arms can be closed, tells me the relays would be closer than "normal" to perpetuate this myth of invulnerability.
 * First: Why is Sovereign taking 10-15 minutes to get to the Citadel from the relay a "fact?" I don't recall a timer during the sequence. You can time it yourself. The entire sequence takes about ten minutes to get through in real-time, if you move as fast as possible in-game.
 * Gameplay and Story Segregation versus Take Your Time. Just so you know... It takes less than 4 minutes (My best time was 3 minutes and 38 seconds) to get from the end of the initial video to the ramp down to the mass relay on easy mode. Then less than 60 seconds for the ramp, then another 30 seconds to get to the elevator (by which time Sovereign is inside the Citadel, and attaches himself to the tower). This is not killing anything (but those two husks by the elevator), and just driving through (granted it does take a little practice). I'll admit that it could be 10 to 15 minutes (I disagree, but it's possible I'm wrong). But it is certainly not a fact.
 * The Citadel was not built to be a fortress. Yes, it is. It's built for the specific purpose of being the perfect place to establish a government, and that includes an impervious outer hull that cannot be damaged in order to protect that government, to make it even more valuable as a center of government. A structure that can close itself up to protect its occupants is pretty much the definition of a fortress - and the Citadel acts as one until the Reapers don't want it to be one.
 * "Acts as one" can also be said in 2 words "looks like." Which is what I said. The Citadel looks like a fortress. As you said, when the Reapers "don't want it to be one," the Citadel is not a fortress. Ergo, the Citadel is not a fortress. It looks like one, but it was built to be a trap.
 * It is a fortress. Just not one that works against Reapers because they built the damn thing. The only reason that Sovereign was able to get into it was because Saren let him in and then closed the arms around him. Normally the arms would seal and it would take " several days of sustained bombardment to inflict any serious damage to the superstructure."
 * Again, looking at the Codex, the asari had 21 Dreadnoughts available to them, the turians 37, and the salarians 16 (as of 2183). Only one Dreadnought was present at the Battle of the Citadel... Now that I think about it, the fleet present was less Awesome but Impractical and more "severely underestimating Sovereign to the detriment and death of those involved."
 * No. There were at least five turian dreadnoughts as well, judging by the size of the vessels that were positioning themselves between Sovereign and the Citadel. We know Sovereign is two kilometers or longer, so there is absolutely no way the ships that it rams are anything less than dreadnoughts based on their size compared with it. In other words, the Citadel devoted at least five turian dreadnoughts and one asari, that we know of - there appear to be more, too.
 * One cannot claim, as one does above, that the proximity of the Citadel to Sovereign is due to a trick of perception and size (which I'll concede is possible), and not believe the same could be said of the Citadel fleet. Other than the Destiny Ascension, none of the ships in the fleet are larger than the geth dropships (which are classified as frigates, according to the Codex). I highly doubt that turians have built dreadnoughts the size of frigates.
 * Look at the size of the turian ship Sovereign rams here at 1:45. There is no possible way that is a cruiser; it is at least a kilometer long, as we know Sovereign is more than two kilometers in length. And there are five of those ships visible in the frame at 1:24.
 * I ask you to watch the same video you presented. There are, in fact, eight visible in the frame at 1:24 (one blows up 2 seconds later). There are also ten (of the same design as those eight) seen from 0:24 to 0:30 (one of which blows up). My personal favorite is 0:35 to 0:41, where one can pick out 16 ships of the exact same design as the "so-called" dreadnought Sovereign rams. There are also 5 turian ships, of the same design, in the 1:40 to 1:51 section (two explode). But the most interesting aspect is 1:52 to 1:55. Where Sovereign passes these SAME FIVE SHIPS at a different angle, and is 10 times the size of them. So please... Either, there were in fact (at minimum) 10 turian dreadnoughts (and as such dreadnoughts hereby suck at any sort of space warfare, since Sovereign didn't fire a single shot during that entire sequence and all destruction was caused by geth dropships), or each of those turian ships were frigates or cruisers (the more plausible option). Keep in mind, that even though (in the Renegade ending) 85% of the Citadel fleet is destroyed, the turians have two more dreadnoughts in 2185 (Mass Effect two) than they did in 2183 (Battle of Citadel). Final note: Mass Effect Wiki declares that the ship at 1:30 (presumably one of the ones that are present during the ramming situation) is a cruiser.
 * Mass Effect 2 indicates that the turians lost dreadnoughts in a news report if the Destiny Ascension was destroyed. They've decided to exceed previous maximums.
 * Presumably, the Citadel fleet was largely out of the system on those patrols mentioned, and could have returned pretty quickly if the Mass Relays were still operational. They weren't, hence why the geth fleet overwhelmed the defenders.
 * On this point, how was the attack a "surprise" at all? The Turian fleet was out patrolling all major access points to citadel. If the Geth moved through one or all of those relays wouldn't somebody have reported it? Even more so, a giant Geth fleet isn't a common sight in citadel space much less a Hulking Giant Mecha Space Cthulu Of The Coming Apocalypse. Somebody had to have reported it at some point.
 * No, no, no, no no no! People keep saying this, and it's wrong. The fleets were not defending "all access points to the Citadel." The turian Councilor explicitly says that they're guarding all relays connecting Citadel Space to the Terminus systems. Sovereign and his geth ships simply used a different relay, most likely one of the countless that are left inactive.

The Other Spectres

 * Why are there no other Spectres working on assessing and countering the geth? There should at least be some gathering intelligence, yet you never hear anything about it?
 * Until Eden Prime, the geth had isolated themselves for three hundred years, in an area without known and active Mass Effect Relays or communication subrelays. Barring those devices, getting a message from the Veil to the Citadel could take weeks, and it's not clear there would be much to say. The geth don't speak in a way that universal translators like, and even killing one is unlikely to give any useful information. All you could really find out is production schedules. And that would be the real risky part. The geth weren't part of the Council's limit on destroyer manufacture, nor did they seem to care about the other Council races, only those space-gypsies trying to shut them down. The Council was being stand-offish and avoiding the Veil and the Traverse specifically to keep things that polite because their military might well not have been able to win, and sending spies in would only encourage military action.
 * Um, the quarians lived beyond the Veil and were part of galactic society for centuries. Liara also mentions that the quarians activated more dormant Mass Relays than any other Citadel race. The issue isn't that there are active Relays beyond the Veil, it's that the geth never used them to get beyond the Veil. And they probably destroyed any non-geth ship coming into those Relays they controlled, figuring it was the start of a Citadel invasion.
 * Plus, the galaxy is pretty damn big, and I doubt the geth are the only worries on the Council's agenda - especially as the geth present no threat to any Citadel species except the humans, and the Council makes it pretty clear they don't give two shits about the loss of human colonies. The Council acts a lot more concerned about not riling up trouble with the Terminus Systems than they are about the geth anyway, which is the primary reason they never raise a finger to help the humans and don't want to interfere with the geth.
 * No, this still doesn't make sense. After the geth beat the crap out of the quarians, why the hell would the species assume that they weren't next on the agenda? I mean, given what they did to the krogan and rachni, a preemptive strike against the geth would be par for the course.
 * Uh, the Council did what they did to the krogans and the rachni because they were a serious, expanding military threat. The geth, on the other hand, stayed on the other end of the Perseus Veil for three hundred years without bothering anyone. There's no reason for the Council to bother the geth, and starting costly wars for no really justifiable reason is not the Council's modus operandi. Even the salarians only launch preemptive strikes when they know an enemy is planning an attack.
 * Also, the geth's territory is located on the opposite side of the Perseus Veil, and the Veil is on the far side of the Terminus Systems. In order to attack the geth, you'd have to either pass through Terminus or move close to them, which will result in full-scale war with the Terminus Systems either way.
 * All that being said, there is a big feeling of "One Riot, One Ranger" to the game.
 * "Why are there no other Spectres working on assessing and counter the geth?" Who says there aren't? Just because you never hear about it doesn't mean it isn't happening. And honestly, did you really expect to hear about it? These are Spectres we're talking about. Secret black-ops stuff is pretty much their whole bag. Plus, most military organizations tend to practice a little thing called "need to know". If another Spectre stumbles across some valuable intelligence Shepard can use, the Council will let him know about it. Otherwise, well, Shepard doesn't really need to know how many Spectres are also tracking the geth or where they all are.
 * Yeah, but knowing where other Spectres aren't is pretty useful. They imply in-game that some Spectres prefer to just blow a place up if it gives then a problem. That would suck if an independent Spectre was in there...
 * Well, the Council does give you a specific list of planets to check out (Feros, Therum, & Noveria). If another Spectre was on any of those worlds the Council would probably send Shepard elsewhere.
 * Maybe the rest of the Spectres are on assignments they can't be pulled away from? Anderson admits they have no idea how many Spectres there are, only a rough estimate of "under a hundred". Not to mention they don't particularly care about the raid on Eden Prime or the geth until they learn that Saren had gone rogue.

The Normandy, The Shuttle, and Viewports

 * Why are there almost no vehicles or ships with forward viewports? If you go to the bridge/cockpit on any ship-based quest you can see it's totally enclosed with no windows or viewports (there are viewports in the ship but never in the cockpit area for some reason). The only ship I can think of with forward viewports is the Normandy, but they don't seem to serve a purpose since they don't cross the pilot's field of vision. It seems that pilots have to rely solely on their instruments and ship sensors to fly. Isn't that inefficient? Not to mention dangerous? What happens if the console shorts out or the sensors are damaged by space debris? If one of the instruments is miscalibrated or knocked out of alignment, how is the pilot supposed to know without any visual reference point to compare with?
 * Because windows are dangerous. Space debris can puncture windows and destroy them, and they offer potential weakpoints for kinetic weapons in space combat. There's a reason why actual spacecraft like the Space Shuttle or actual space stations like ISS don't actually have windows. Not to mention windows are completely useless in spaceflight when you're moving so fast you can barely see objects approaching at visual range, and point-blank "knife-fight" range occurs at tens of kilometers, with most combat occurring at hundreds or thousands of kilometers. Pilots rely on their sensors because those are the only practical way to see their surroundings. Even in modern aircraft, pilots rely mostly on instrumentation over visuals.
 * Um, what? The Space Shuttle DOES have windows. They're not very big, but they do exist. A military vessel without windows can arguably be justified, but a civilian cargo freighter can't. Modern aircraft pilots do rely on their instruments but there is a reason the planes still have windows. Because if the instruments fail, the pilots have to rely on their eyes to navigate. What happens if a ship gets winged by a meteor that disables their sensors? How are they supposed to land to make repairs if they can't see anything?
 * Yes, it DOES have windows, which are used primarily for landings and for docking with the space station. These windows are actually three panes thick (a pressure pane on the inside, then an optical pane in the middle, and the outer pane is a thermal pane), made of aluminum silica glass and fused silica glass; the thermal pane has a high-density, temperature-resistant acrylic as part of the mix. EACH of these panes is about three and a half inches (~89 mm) thick. And yet... a fleck of paint no more than 0.08 inches (0.2 mm) in diameter punched a pit a few inches deep in one of those window panes. That's with the shuttle orbiting at about 17,500 mph (28,165 km/h), and there's no telling how fast the paint fleck was going. And that's not even close to the speeds a ship in Mass Effect can travel. Now, I know your argument does not necessarily include the ship taking damage, just all the sensors failing at once. But, just for a moment, let's assume that the ship's taken so much damage that not only have the sensors failed, but the kinetic barriers (shields) have failed. Now those windows are a hull breach just waiting to happen as soon as so much as a fleck of dust hits them. (But then, the AI in Mass Effect 2 pointed out that the windows also have closeable shutters, or something like that.)
 * If every single one of the ship's sensors are knocked out by a meteor impact or something similar - which isn't going to happen if the ship is reasonably engineered by anyone with a modicum of competence - then the ship has probably already taken enough damage that it's more or less fucked in the first place. Unless you honestly believe they aren't going to have a sensible engineer who designed the thing with multiple cameras and sensors in case it took damage. And most civilian ships are going spend most of their time in deep space; if they take massive damage like what you're suggesting out in the middle of nowhere, they're already fucked, and they're probably not going to be anywhere near a planet, let alone one suitable for landing, let alone one with facilities to deal with them if they try to land - and any planet with such facilities can easily be contacted and help sent to the ship without it needing to try and land. That's exactly one of the things brought up if you take Garrus' sidequest in the Citadel Tower. Not to mention that if the ship is sufficiently capable of conducting repairs on itself on a planet, then it should have the capacity to do those same repairs in zero-gravity - unless you honestly think that a society that has ships that operate in zero gravity wouldn't design their repair equipment and train their engineers and technicians to operate in zero gravity as well as on a planet's surface. In fact, there's really no reason for a damaged ship to land on a planet unless there's repair facilities on the ground, and if there are, then they can send for help from said planet and help can arrive to assist them.
 * Okay, I'll grant you one point. It's unlikely that all of a ship's sensors would be simultaneously damaged. However, my point still remains. What if the navigational equipment malfunctions? Without any way to see out of the ship, how is a space pilot supposed to know that his sensors aren't working properly? Modern aircraft have gone down in flames because one sensor wasn't working or wasn't aligned properly. A space ship in the Mass Effect universe could be barreling right into an asteroid field and be blissfully unaware of it because their proximity sensors have gone down. "In fact, there's really no reason for a damaged ship to land on a planet" What? There's plenty of reason for a damaged ship to land on a planet (or at least a space dock) rather than for the crew to try and fix the ship themselves. Namely the fact that space is an incredibly dangerous environment to work in. If you were a ship's mechanic and you had a choice between going on a spacewalk to fix a damaged sensor and setting down on a planet or pulling into a space dock with a pressurized repair bay, which would you choose? Also, there's a very good reason why the standard procedure for any modern ocean-going vessel is to immediately head for the nearest dry dock in the event of damage. Because if the problem suddenly gets worse you can end up stranded in the middle of the ocean on a possibly sinking vessel with no one around to help you.
 * Not to mention that if the sensors are disabled, the ship can simply point itself toward the nearest colony or inhabited planet and zip over for repairs, if they cannot repair their own sensors. Since there are no FTL sensors in this setting, losing their sensors isn't going to impair their navigation much in the first place.
 * Point itself to the nearest colony how? Autopilot? What if that's down too? Or what if the autopilot is up but the navigational computer is down? How is the autopilot supposed to even find the nearest colony, much less get to it? And even if the autopilot can find its way to a nearby colony, does it really seem wise to trust the lives of everyone on board to the autopilot's supposed ability to land the ship? The autopilot in a modern passenger jet can theoretically take off and land the plane itself, but every pilot on Earth knows better than to let the autopilot land the plane for them.
 * How is the pilot supposed to find the nearest colony just by looking out of a window? Space is BIG, have you ever seen the "Pale Blue Dot" picture, taken from well within our own solar system but showing Earth as a tiny point of light. And all of your arguments seem to hinge on the ship taking a remarkably specific level of damage, enough to destroy all the sensors and autopilot, but not the engines or life support and certainly not enough to break those glass windows you insist on putting in the front.
 * "How is the pilot supposed to find the nearest colony just by looking out of a window?" How is the autopilot supposed to find the nearest colony if the navigational computer is down? At the very least a living pilot can try to pinpoint a star or star cluster where he knows a colony exists and head in that direction at FTL speed. But without a viewport to see out of he can't even do that much. A ship with its sensors disabled and no viewports is effectively blind. "And all of your arguments seem to hinge on the ship taking a remarkably specific level of damage, enough to destroy all the sensors and autopilot, but not the engines or life support and certainly not enough to break those glass windows you insist on putting in the front." Funny, all your arguments seem to hinge on completely ignoring mine. My arguments do not "hinge" on anything of the sort. I asked what happens if certain systems go down while in transit, not what happens if a ship suffers remarkably specific damage. (Though for the record, I think you're overgeneralizing when you claim that any damage sufficient to bring down the shipboard sensors would automatically bring down the engines or life support. Especially considering those systems would be located in completely different areas of the ship and would certainly have much greater protection from outside damage since they're so important. As for the windows, spaceship windows tend to be thick and durable specifically so they can stand up to outside damage, whereas sensors tend to be much more delicate.) Regardless, damage is just ONE example of how a system can be brought down or malfunction, there could be any number of other reasons. What if there's a power surge that burns out one or more sensors? What if EM interference disables the sensors? What if a sensor is just miscalibrated? How will the pilot ever know if he can't see outside the ship? Again, a ship could be barreling right into an asteroid and if the proximity sensor is malfunctioning the pilot would never know it because he can't see outside the ship. And again, if the sensors are disabled how does a pilot land the ship? How does he even pull into dry dock for repairs if he can't see where he's going? What is he supposed to use, the Force?
 * "At the very least a living pilot can try to pinpoint a star or star cluster where he knows a colony exists and head in that direction at FTL speed." That is a recipe for disaster. Flying FTL speeds using only sight is a very, very stupid thing to do. Joker even points this out. The reason there are no windows in the cockpit is the same reason the Normandy doesn't go invisible to our eyes when its stealth systems are activated. When you are flying through space, everything is so far apart that using visual markers is completely pointless. Distance is measured in kilometers at the smallest, way too far for any human eye to pick out when stationary, let alone traveling at FTL speeds.
 * Additionally, the game goes to lengths to explain how at FTL speeds, everything is blue or red shifted, rendering windows utterly moot, as visible light will be shifted up or down into wavelengths invisible to the human eye.
 * "What if the navigational equipment malfunctions? Without any way to see out of the ship, how is a space pilot supposed to know that his sensors aren't working properly?" There's a thing called a diagnostic. It's usually run when you need to see if something is malfunctioning. And how is looking out the window going to help him see if his sensors are malfunctioning when 99% of the time he's traveling between systems at FTL speeds?
 * "Modern aircraft have gone down in flames because one sensor wasn't working or wasn't aligned properly." Well, then those windows they had didn't seem to do them much good then, did they?
 * "A space ship in the Mass Effect universe could be barreling right into an asteroid field and be blissfully unaware of it because their proximity sensors have gone down." You know that most asteroid fields aren't The Asteroid Thicket, right? And that most asteroid fields in this setting are already logged, so even if their sensors are down they'd know where they were in a system?
 * "There's plenty of reason for a damaged ship to land on a planet (or at least a space dock) rather than for the crew to try and fix the ship themselves. Namely the fact that space is an incredibly dangerous environment to work in." And 99.999% of all planets in Mass Effect are also just as dangerous to work in too. Did you not notice that of all the worlds you land on in-game, almost all of them required you to wear pressure suits, too? It would be easier to repair the ship in zero gravity than attempt to land in a potentially dangerous alien environment.
 * "Also, there's a very good reason why the standard procedure for any modern ocean-going vessel to immediately head for the nearest dry dock in the event of damage. Because if the problem suddenly gets worse you can end up stranded in the middle of the ocean on a possibly sinking vessel with no one around to help you." Space is not an ocean, so ocean-going vessels' procedures do not apply that well. Repair docks are few and far between in deep space, as opposed to plentiful numbers of repair facilities along the coast of any reasonably civilized country on Earth. A ship that breaks down either needs to repair itself or it's dead in space, with or without sensors. And if their sensors are damaged and they're outside a system, there's nothing windows would help them with.
 * "How is the autopilot supposed to find the nearest colony if the navigational computer is down?" Red herring. You're still not explaining how being able to see out a window will help them navigate between systems.
 * "At the very least a living pilot can try to pinpoint a star or star cluster where he knows a colony exists and head in that direction at FTL speed." And if his sensors are down and he has no idea what's there? If his navigation is down and he may not even be sure he's looking at the right system? Being able to look out a window will tell him he's looking at pretty lights, something a camera can tell him just as easily.
 * "What if there's a power surge that burns out one or more sensors? What if EM interference disables the sensors? What if a sensor is just miscalibrated? How will the pilot ever know if he can't see outside the ship?" Systems like that are generally designed with warning systems built into them if they malfunction. It's commonplace. And a pilot going into space without previously ensuring his sensors are properly calibrated deserves what happens to him.
 * "How does he even pull into dry dock for repairs if he can't see where he's going?" They're called "tugs."
 * Regarding the possibility of running into an asteroid, space is not only big it's also almost entirely empty. You are very unlikely to hit anything at all that you weren't specifically aiming for. As for EM interference or a power surge knocking out all the sensors, as previously mentioned, any competent engineer is not going to design the ship without multiple backups, and the whole point of backups is that they are protected from anything that is likely to destroy the main thing. In particular, if you put the backup on the same circuit as the main sensors so that a single power surge could blow both then you deserve to be stranded. As for landing, who says they have to land? There is really no reason to try to land a heavily damaged ship - they have their own engineers and repair systems, and if that is not enough they could call for help from the planet they were trying to land on and have them send assistance. Maybe there are some convoluted circumstances where being able to look out of a window would help, but these need to be enough to justify including a large vulnerable portion of the hull made out of glass, and having your pilot and possibly other critical crew members stay at the front of the ship next to the weakest section of the hull where a single missile could kill them, rather than buried away in the centre where they belong. Also, with the exception of landing, every situation you have described so far could be solved by suiting up and going out of an airlock, giving a greater field of vision (compared to a window that can only look forwards) and without introducing any weakness to the hull.
 * Also: periscopes (or even better, photonic masts). The presence of which would render this whole discussion pointless. Sure, they're not mentioned, and if they exist on starships it's probably as a fail-safe of the fail-safe of the fail-safe, but when you get right down to it, a periscope/photonic mast is probably even more useful on certain types of spacecraft than it is on a submarine, so I doubt they'd do without it. All the ability to see outside, without the dangers of EVA or honking great glass windows (which would have a far more limited FOV anyway).
 * Even better: external cameras. There's nothing windows do that a a solid array of external cameras (with backups, naturally) would do better.
 * As far as a damaged ship going to a planet-based facility. That's just stupid - atmospheric entry is one of the most dangerous parts of a mission. It would be safer for everyone on board to dock in space and repair it there. And as far as trying to point a ship in the right direction and then coasting there? Also stupid as even a very small error in degree would result in missing the mark by millions of miles - Joker says as much in the intro that getting within a few tens of thousands of miles of the equivalent of needle's head over a distance of several hundred light years is an exceptional job.
 * In the first book (Ascension or something...), it makes reference to the fact that human ships still subscribe to the romantic design of having their cockpits at the front, with windows to see out of, instead of somewhere sensible, like in the middle. So it's more aesthetics than function.
 * The second game actually has a reference to this conversation: Shepard can point out that a window is a vulnerability in a ship's armor, and EDI can reply that this objection was expected and that the observation bays can be depressurized and have armor plating that will extend over them in combat. As well, the bridge windows have a usable switch that will close armored shutters over them. The conversation basically screams "Are you happy now, Internet?"
 * Not to mention that although the bridge is up front, the CIC is nice and "safe" within the centre. Just like a modern oceangoing warship. Though considering there's no discernible door between the two, one wonders just what difference it would make.
 * Windows are useful whenever your spacecraft is somewhere other than space.
 * Most spacecraft stay in space. And as was pointed out above, there's nothing a window can do that a series of cameras and sensors can't.
 * This has been touched on, but bears expanding: Regarding FTL travel and the immense size of space. The closest star to Sol (Proxima Centauri IIRC), is roughly 4.3 light years away. That's 4 years and 4 months, traveling at the speed of light, to get to the closest star. Every time a spacecraft is traveling in interstellar space, it will be at speeds far exceeding light speed. It is noted in the Codex that sensors operate at the speed of light. Ergo, any interstellar jump must be plotted out and obstacles accounted for in advance, because at that speed you'll hit them before it's even possible to see them. A window serves no practical purpose in deep space. The only time you're traveling at sub-light speed is within a star system, where presumably there will be a repair station within hailing distance if your sensors or navigation systems malfunction. If not, you can call a "tow truck". Even within a star system, objects are far enough apart that you shouldn't be within visual distance of anything by accident. The moon's average distance from Earth, for example, is 384,403 km, compared to the actual diameter of Earth, which averages 12,756 km. So the only remaining time a window might be useful is when pulling off the kind of maneuver that Joker does when he drops the Mako. Frankly, if you fry your sensors in the middle of that, a window isn't going to help you much.
 * The Normandy's engineer explicitly states that the reason the stealth systems can still be called such even though they don't make the Normandy invisible per se is because a visual scan (i.e. looking out the window) in space is unfathomably ineffective, thus creating the presumption that any windows that a ship has in the first place are purely for decoration. Not to mention that if you're building a spaceship it makes vastly more sense to stick a camera on the front than to put a window there, since if a random piece of space debris one hits while flying at FTL cracks a camera it will be far less destructively bad then a crack in a window where that window is the only thing separating everyone inside and the cold vacuum of space.
 * Cameras are also a whole lot smaller than windows. The chances of debris (or weapon fire) hitting a camera are so much smaller than that of a window. Not to mention with multiple cameras positioned all over the hull, a pilot can potentially have a fantastic view of any part of the ship he wants to look out of, in any direction, at any time. Heck, modern CARS have cameras in the back. I'd guess that in nearly ever Mass Effect ship, hundreds of cameras are positioned on the hull in varying positions. How else would you park a capital ship? Certainly not by looking out a window.

Warfare and The Technology of War

 * The starting armour of your character, Kaidan and Jenkins is dark grey, as is the armour of the Alliance marines seen during the listening post assignments. So why is Ashley's starting armour bright white and red? It could be that her superiors would see her dead because of her background, but that seems unlikely given that she never got hardship posts. Plus, the rest of her unit was presumably equipped that way.
 * Also, why is it that so many sets of armour completely eschews camouflage in favour of lurid colours? There is a blue and white set, solid reds and solid blues, a white and orange set for Tali and a bright yellow one. Active camouflage is being developed today, surely the technology would be mature by the time of Mass Effect?
 * When people have man-portable tracker units capable of spotting any moving enemy within X hundred feet, is visual camouflage really worth anything? Remember, any suit of armor has to have an energy shield up, which makes it entirely detectable to instrumentation.
 * So basically, they just say "screw stealth", essentially because it's nearly impossible to sneak up on anything with a radar.
 * However the only possibility of stealth action is using a sniper rifle from very far. It's work because the radar systems have a limited range. In that specific case, it would have been better to have a camo.
 * True, but not relevant for purposes of this discussion, as Ashley's unit on Eden Prime were garrison troops/military police, not snipers.
 * Radar systems can be jammed. In fact, the geth do exactly that several times throughout the game. Neglecting basic camouflage because you think your radar technology is infallible strikes this troper as a very foolish idea.
 * And even the worst of geth jamming fails before a level X scope. There is also that the geth themselves obviously don't believe in camouflage, given that they have flashlight heads.
 * "And even the worst of geth jamming fails before a level X scope." Maybe so, but what if you DON'T HAVE a level X scope? Level X scopes are the most expensive and powerful scopes that exist in the entire game, after all. There's no reason to assume every soldier in the galaxy has access to them. And even if we assumed they did, there's no reason to assume the geth (or someone else) won't figure out how to generate an even more powerful jamming field capable of defeating even a level X scope. As to your second sentence, the geth's inability to properly camouflage themselves is not the point. The point is that radar is not infallible and it would be foolish to assume otherwise. There is simply no good reason at all for a professional military organization to purposely forgo basic camouflage.
 * Note that "radar jamming" doesn't actually prevent detection of enemies, it just blots out your minimap. They'll still be displayed and targetable on the main screen as normal.
 * With the incredible number of varied planets one travels to in-game, exactly what sort of camo would be useful for more than a handful of them? Dappled forest pattern is pretty useless on planet covered in aluminum dust. There's really no point in bothering with stealth gear.
 * There's also the fact that most engagements in this setting happen at relatively short ranges. There really aren't going to be many long-range infantry engagements in the Mass Effect setting, what with the prevalence of orbital assets and armored vehicles. Infantry combat is going to be, almost exclusively, close-range combat, likely inside structures, where the color of your camouflage is going to be useless.
 * Shepard, Kaidan, and Jenkins are on a one-of-a-kind prototype ship being sent on a covert-ops mission with a Spectre; whereas Williams has a low-prestige post on a peaceful, idyllic planet, providing security for farmers. (As Ashley's back-story reveals, her posting on Eden Prime is the result of her family being blackballed by the military, which means the planet or her specific unit is not a desirable post.) It's likely that Shepard and the Normandy's crew have "better" equipment reflecting their status, or at least armor that appears stylized for covert ops rather than parade-ground spit and polish. Note that Ashley's starting armor is one of the crappier types; many of the "best" models have some form of camouflage pattern to them. Others, like the bright red Mercenary line (the default color for Wrex) seem colored for style and impact rather than concealment. In any event, it's likely that basic equipment isn't uniform across the Alliance military--especially considering the Normandy's merchant-as-supply-officer--and that different units may have different suppliers depending on their need, prestige, and maybe even the personal wealth of their officers.
 * It could have also been a simple case of camouflage color screw-up. During Operation Iraqi Freedom, the US Marines' First Force Recon were issued MOPP uniforms in forest green camouflage. It's entirely reasonable that Ashley would have gotten shafted with Phoenix armor due to supply problems, and from the video of the raid on Eden Prime, it looks like the Alliance Marines already wore a mish-mash of uniforms, including one gray and white one and one yellow and gray.
 * The Canadian Armed Forces showed up in Afghanistan with nice forest-y uniforms, too.
 * To be fair, this troper is pretty sure certain color combinations would qualify as camouflage on certain planets.
 * This is a perfect example of Rainbow Pimp Gear These armours are all different models made by all different manufactures in all different regions by all different races of aliens (this troper finished the game wearing a bright red affair that was made by a "volus manufacturer based in the Terminus Systems." Surprisingly well-made since they got the shape right for the female Shepard). Some may be designed based on alien philosophies similar to the Napoleonic era when different armies wore different colors to avoid freindly fire, others may have superstitions like certain colors bring good luck, while others are cursed, and some may be designed for camouflage on a certain planet. Many may even be costume showing off the pirate groups "gang colors." This doesn't really matter, since whenever Shepard buys anything it's "show me what you have." The merchants may have bought it second hand, or it may be meant for use on a specific world, but since most players go for defensive or mobility bonus, this doesn't realy matter, also consider that many armours can only be obtained by looting abandoned bases out on the frontier, and this more than explains the lack of camo.
 * Unless Shepard is the only one in the galaxy equipped with sensors and a HUD, any camouflage is probably very much irrelevant. You can't hide from the red triangles.
 * Precisely. Traditional camouflage would be irrelevant in the Mass Effect universe. The extravagant colors and styles would be analogous to makers' marks or logos (including the armors that DO display traditional camo patterns). And any enemy force that ISN'T using advanced HU Ds or computer-assisted targeting would also lack the technology to put so much as a scratch in that armor.
 * Wouldn't this also depend on the colour vision of the different races? The chances of any two races seeing in the same parts of the spectrum would be pretty slim, making it even harder to come up with effective camouflage. I bet the geth can see infrared.
 * I interpreted it as a subversion of the Pink Girl Blue Boy trope. Ashley Williams comes onto the screen as a damsel in distress, firing a pistol and yelping helplessly while pursued by mooks. Seconds later, she takes cover like a pro, whips out an assault rifle and turns out to be the all-combat character. After dropping that piece of crap starting armor, you don't get anything pink for her again.
 * I thought it was due to her posting. Shepard is in an active combat role, despite the official story on the shakedown run. His armor is based on the need for dull, hard to spot colors. Williams, at the game's start, is posted as essentially military police in a burgeoning colony. Her job involves working with civilians and tamping down trouble spots. The armor may well be designed to be more visible, so civilians can spot it. After all, they never expected an attack.
 * This troper sort of Fan Wanked a lot of the "armor" in the game to being space suits manufactured for extra vehicular activity and operations on Death Worlds rather than full military or police armor. C-Sec all wears the same colors, and so do the mooks on Normandy, hence the presumption that alot of the armor was really not anyone's standard issue fatigues.
 * It could similar to the real world - there might be basic armor given out, but then soldiers are free to buy additional equipment for themselves, eating the costs themselves. Given the much more modular nature of armor in the ME universe, it could even be that as long as a soldier's armor meets a certain defensive rating, they can wear whatever they want.
 * Shepard & Kaidan's starting armor is the crappiest in the game. Phoenix armor isn't great but it's not the worst. For example, it's the only armor with built-in health regeneration. I have on occasion had Shepard switch armor with Ashley because hers is better.


 * Why does the game spend so much time going on about ships, technology and tactics and only make the only space battle a giant slugging match?
 * All the Codex stuff is nonessential. It's just there for backstory and world building. It goes into extensive detail about salarian comat doctrine, for example, but we never actually see salarians fight - it's just there so you can read it if you want.
 * Not to mention the Codex explains why the space battle isn't like Star Wars.
 * And yet the only space battle actually shown IS just like Star Wars.
 * Well, yeah. The only space battle shown in the first game occurs at extremely close range because of the limitations of the spatial "terrain" they're fighting in. When you're at close range, you use close-range tactics and weapons. I don't get the issue with this; it's like watching a knife fight in a phone booth and wondering why they don't fight with rocket launchers instead.
 * The Codex does go into "knife fights", space battles that are fought near mass relays and other important areas. So makes sense for the Citadel fleet to protect the 13+ million living in there. Plus they WERE ambushed (kinda) so they didn't have the time to move out a few hundread kilometers.
 * They wouldn't have been able to move out that far. The Codex talks about the Serpent Nebula and how dangerous it is to navigate. The only safe way to reach the Citadel is through the Mass Relays that orbit it, and in the two instances we see ships exit a Relay and approach the Citadel, they don't travel far - somewhere between 50 - 100 kilometres, at most.
 * Mostly to prevent fans from making IJBM pages and picking apart their logic. It seems they failed.

The Genophage, The Rachni, The Virmire Assault (Warning: Wall of Text)

 * This troper found having to convince Wrex the genocide of his people's a good thing a moment that terminated the final vestiges of moral choice he sensed he had in the game. Exterminating the rachni is a Renegade move but ruining the krogans' chance of recovery is necessary for Renegades and Paragons. Obvious possibilities like copying the data for use elsewhere/when or holding the location don't even come up.
 * Because unlike the Rachni Queen, who at the very least promises to be peaceful and her death will result in the extinction of an entire species (effectively, you're sentencing her to death for something she herself is innocent of, based on the reputation of her species) the krogan have, time and time and time and time again, proven themselves to be unsympathetic, violent, bloodthirsty bastards. The krogan are practically physically incapable of not being sociopathic, aggressive, and expansionistic. Wrex himself points out that the krogan are so violent and selfish that they cannot even organize themselves to find a cure for the genophage on their own. The krogan were bad enough before the genophage was unleashed, and after it was unleashed they became even more destructive and violent. Curing the genophage at that point would effectively result in the resurgence of the krogan, but instead of as a violent and expansionistic power of hyper-adaptive, rapid-breeding naturally-evolved supersoldiers, you'd have all of the above combined with a healthy dose of savage bitterness, hatred, and complete disregard for sapient life.
 * "Because unlike the Rachni Queen, who at the very least promises to be peaceful" Oh, she promises to be peaceful? Well golly-gee-willickers, that changes everything. If she promises to be peaceful, by gosh she must be telling the truth.
 * "her death will result in the extinction of an entire species (effectively, you're sentencing her to death for something she herself is innocent of, based on the reputation of her species) the krogan have, time and time and time and time again, proven themselves to be unsympathetic, violent, bloodthirsty bastards." I'm sorry, did you actually read that before hitting the save button? Since when did all krogan prove themselves to be unsympathetic, violent, bloodthirsty bastards? How is infecting all krogan everywhere in the galaxy with the Genophage, including females and children who never hurt another sapient being in their lives, anything but judging them based on the reputation of their species? I defy you to provide any justification for unleashing the Genophage that can't also be used to justify wiping out the rachni.
 * The argument here is not whether the original genophage's use was justified. The argument is what the difference is between killing the Rachni Queen and destroying a "cure" for the genophage supplied by Sovereign. One is simple, outright murder; the other is the elimination of a strategic tool for use by an obvious aggressor intent on subjugating the galaxy. They are not comparable.
 * However, if you want to argue the morality of the genophage...note that one of the krogans' primary strategic advantages is sheer population growth. This is explicitly stated as one of the critical strategic advantages the krogan have. Removing that advantage was significant enough that it actually turned the tide of the entire war. Thus, targeting the krogans' ability to reproduce was a strategic act of war, and had nothing to do with "judging them based on the repuation of their species." Note that the genophage didn't kill anyone; it simply eliminated the krogans' ability to replinish their supplies of soldiers. The krogans' ability to replinish their numbers, in overall strategic terms, was on the same level as their industrial capability to arm their soldiers, and being an explicit and critical advantage, that means that in a wartime scenario, targeting the krogans' capacity to reproduce was a justified act of strategic warfare. Of course, once the war was over, there was no reason why the salarians couldn't develop a cure for the genophage, but then that would simply result in the krogan warlords who started the war turning right back around, rebuilding their armies with fresh troops, and doing the rebellion thing all over again. After all, the Krogan Rebellions started because the krogans' population was rampant and uncontrolled in the first place.
 * That's one pretty fine moral hair you're splitting. The fact that the krogan's prodigious birth rate was a significant military advantage for them does not in any way abrogate their right to reproduce. China's population is several times that of the United States. If the People's Republic of China and the United States of America ever went to war, China's ability to throw wave after wave of soldiers at us would be a significant military advantage. If the Chinese proved unwilling to negotiate for peace, would the American military be morally justified in unleashing a chemical weapon that permanently sterilized the entire Chinese population?
 * In a word, yes. Targeting the civilian population in a time of total war is acceptable if they are supporting the war effort. If the enemy possesses a strategic advantage, you target it. Period. The krogan's entire way of war was dependent on their natural prodigious birth rate, and that strategic advantage was a target. The greater issue here may be that after the krogan were defeated, no one bothered developing a cure for the genophage. It may be a classic case of Fantastic Racism in action; the various Citadel species seem to think in terms of species. E.g. all the rachni are evil, or all the krogan are expansionist warlords who'll overrun the galaxy.
 * What? That's incredibly cruel. The krogan aren't robots. They may reproduce quickly, but they're not born warriors. The fast reproduction was a useful starting advantage, giving them vastly superior numbers, but unless the war is lasting for decades, the incredible birth rate would have a rather negligible effect for the war. Besides, with all the racism against krogans at this point, and their natural aversion to being scientists, it's pretty much genocide against many, many innocents, while the Rachni Queen had ancestral memories and the like.
 * The Krogan Rebellions didn't just last decades, they lasted for centuries. Besides, there's nothing in the game that says that the krogan take a long time for mature, they could reach maturity in a year and even be capable of killing a grown human adult before then considering how brutal their homeworld is. And if the krogan are incapable of becoming scientists when a genetically engineered plague prevents them from breeding and ensures their doom in a few generations, face it, they deserve to go extinct. Survival of the fittest in action.
 * Yes, it is incredibly cruel. War is cruel. Especially total war, like the Krogan Rebellions. But that's how war is fought - look at Earth's history and the examples of total war. World War II saw the deaths of many millions of civilians simply because they happened to be located near strategic military-industrial resources. During the Cold War, both sides were fully prepared to wipe out hundreds of millions of civilians because they were located near military resources. In total war, you don't hold back simply because civilians are in the way, you eliminate enemy resources before the enemy can turn them against you. Yes, that is a cold, harsh, and cruel line of thinking, but total war is a cold, harsh, and cruel thing, and when you are fighting for your very survival, you place your survival over your opponents'. The krogans' birth rate is explicitly and repeatedly mentioned in the Codex as being one of their biggest strategic advantages - to the point that its loss led to the krogans' eventual defeat. And in total war, you eliminate your opponents' advantages. If that happens to be their birth rate, so be it.
 * "Targeting the civilian population in a time of total war is acceptable if they are supporting the war effort." IF is the key word here. I agree in principle. IF a civilian is actively, purposely, and voluntarily supporting the war effort, that civilian is an acceptable target in war. The problem is, the genophage is an utterly indiscriminate weapon. In order to justify its use you would have to prove that every single krogan IN THE ENTIRE GALAXY, right down to the very last man, woman, and child, was an active participant in the war effort. I don't think you can prove that.
 * Let me rephrase what you said just a little bit. In order for a human raised in the United States with the social mores of 2010 to justify its use, you'd have to prove that every single krogan was an active participant in the war effort. In Mass Effect, it isn't 2010, the humans weren't involved in that war, and the races that were involved in that war aren't human. Which means they don't necessarily think like humans, which in turn means that they might not need the same justification that you would. In fact, the Codex makes it pretty clear that the salarians and turians don't think like humans do.
 * In a time of total war, civilian populations will be generally supporting the war effort, especially if conscription is taking place. Ditto if widespread impressment into industrial production is taking place. In order to not be contributing to the war effort, you have to completely abstain from interacting with the economy in any way. And a critical strategic resource the krogan had was their birthrate. That basic, biological capability was being used as a weapon by the krogan against their enemies. It had to be neutralized or the war would, at best, never end and at worst the Citadel would lose. What this effect would have on the krogan in the future was ultimately irrelevant at that point in time to the Citadel; the krogan had to be stopped or they would lose. The genophage only requires one justification: total warfare. There's nothing separating it from any other weapon; the vast majority of weapons systems in existence are indiscriminate. Even if you're a civilian completely opposed to the war effort, if you're anywhere near any location with any military significance, you're in danger. It's one of the crueler aspects of war that civilian presence is really rarely ever considered when picking strategic targets in warfare. The genophage may have been indiscriminate, but so are an artillery shell, a missile battery, a nuclear weapon, or a rifle's bullet. Weapons, as a whole, are indiscriminate. If you're going to argue the genophage's deployment was not justified because it was indiscriminate, that reasoning can be applied to any weapon, period.
 * To edge dangerously close to Godwins Law here, look at World War II. Both sides, both Axis and Allies, were engaged in total war with one another. In that conflict, neither side distinguished between "civilian" or "military." Atomic weaponry, firebombing, carpet-bombing, artillery bombardment, etc were done without regard for civilian presence. The priority was destroying the enemy's capability to wage war. From what has been made clear within Mass Effect, the Citadel has a similar viewpoint about warfare, e.g. the turians' occupation of Shanxi, where they orbitally destroyed entire city blocks to take down single Alliance fireteams. It's a brutal and cruel and horrific thing, but in order to defeat the enemy, it is often necessary. One doesn't wage war by half measures, and while the genophage neutered the krogan species as a whole, the only other option was defeat. Are we really going to blame the Citadel for taking necessary steps to protect itself and a dozen client species from a single belligerent species?
 * Aren't we leaving out that the krogan were not hesitating to drop asteroids on turian civilian populations (rendering three entire planets uninhabitable) to force them to capitulate? And that the Codex explicitly states that krogan don't hesitate to commit atrocities to ensure a smooth occupation? The krogan aren't exactly angels, here, and they did resort to "indiscriminate" use of WMD first.
 * The Genophage does not completely sterilize the krogan. It just VASTLY limits their reproductive abilities. The krogan homeworld was a brutal place where every native being had to be as tough as possible to live. Krogan fertility rates had to be significantly higher than those of other races in order to make up for the harsh environment. Wrex's statement about the krogan going extinct takes into account the limited reproduction on a harsh environment, slowing their growth, as well as, supposedly, the majority of krogan giving up and just fighting for money until they die. Wrex gave up trying to convince the various tribes that they had to focus on population growth instead of just running off to kill anything they could be paid to. Wrex at least understood that with determination, the Genophage wouldn't be overcome, but it could be fought while the population had a chance to grow, if krogan would just stop throwing their lives away like they could afford to in the Rachni War.
 * Not to mention that Shepard points out to Wrex that all of Saren's "cured" krogan are in fact his slaves. Given that, plus the part where Saren almost definitely got that cure from Sovereign, this "cure" appears to include indoctrination as a package deal. No. Thank. You.
 * The cure came from Binary Helix. In one of the news reports on the Citadel talks about a krogan group that hired Binary Helix to find a cure for the Genophage and then sued them when they didn't find anything. But seeing how Saren was a major investor in Binary Helix and he later shows up with an army of Genophage free krogan, I think it is safe to assume they did find a cure and Saren merely took it.
 * Not necessarily. Binary Helix was sued for not developing a cure, so it's entirely possible Saren was researching a cure with Binary Helix, and didn't find one through normal means. Or perhaps he suppressed research on the cure so he could use his Reaper-designed one. The "cure" found in the labs on Virmire involved cloning tanks and husks, so I don't think it was a particularly benign sort of cure.
 * "this "cure" appears to include indoctrination as a package deal." Does it? How do we know Shepard was speaking literally? Remember, he said this before they entered the breeding facility. He has absolutely no way of knowing what side effects the cure may or may not have. It's just as likely Shepard was speaking metaphorically (or even just plain bullshitting).
 * Not exactly. In order to get to Virmire, you have to complete either Feros or Noveria - planets where mind-control is more or less confirmed. Not a big intuitive leap to theorize that the krogan under Saren's command are being mind-controlled when you've got outright confirmation from either/both Shiala and Benezia.
 * The big difference between the Rachni Queen and the krogan cure is that, in order to do what you will with the rachni, you effectively have to murder an innocent sapient being who is really guilty of nothing more than being of a particular species and being the mother of a bunch of feral children. On the other hand, with the krogan cure, you don't actually kill anyone who isn't an enemy combatant working for Saren. There's no real victim there except for the krogan species, which would be able to make their own cure if they weren't such complete asshats who probably deserved it. That's why killing the Rachni Queen is so blatantly a Renegade choice, while destroying the genophage cure is a matter of course.
 * "A matter of course"? I'm sorry, are you actually trying to claim that forcibly sterilizing an entire population is morally ambiguous?
 * Red herring. We are comparing the murder of a single innocent sapient versus the elimination of a Reaper-supplied "cure" for the krogan genophage intended to be used as a strategic resource for war. They are not remotely similair. This has nothing to do with the actual act of unleashing the genophage.
 * Okay, so it's perfectly fine for me to let loose a species that once decided to kill every other form of life in the universe because they felt they were inferior, just because while trapped in a cage and totally at my mercy it said that it was going to be nice now. But it'd be pure evil of me to help save a species that once saved the entire galaxy from being eaten by giant bugs and were victims of their natural environment and their physiology? They may be a species of warrior arsehats but you've got to admit the krogan have got a far better claim to existence than the rachni do, they may be expansionist through necessity but at last they aren't xenocidal. Not to mention the entire situation is the damn salarians' fault in the first place.
 * Okay so it's perfectly fine for me to let loose a species that once decided to kill every other form of life in the universe because they felt they were inferior, just because while trapped in a cage and totally at my mercy it said that it was going to be nice now. Provide evidence that the rachni were going to wipe out all other species in the galaxy. They were on a war of conquest, just the same as the krogan were later. But it'd be pure evil of me to help save a species that once saved the entire galaxy from being eaten by giant bugs and were victims of their natural environment and their physiology? Strawman. No one said it was pure evil, and the rachni were engaged in a similair war to what the krogan would later engage in. Further, you say that the krogan were victims of their physiology and environment, yet the rachni lived in similair environments and spread at similair rates, yet you say they engaged in a war because they felt the other species were "inferior"? Proof of this, please. They may be a species of warrior arsehats but you've got to admit the krogan have got a far better claim to existence than the rachni do, they may be expansionist through necessity but at last they aren't xenocidal. Again, no proof the rachni were xenocidal, and no proof the rachni weren't expanding through necessity themselves. Not to mention the entire situation is the damn salarians' fault in the first place. Strawman. Why does the salarians' uplifting of the krogan have anything to do with this, and what difference is there between the salarians' uplifting of the krogan and the explorers' stumbling upon the rachnis' mass relay?
 * The burden of proof shows the rachni weren't xenocidal; they weren't even fighting of their own free will. On Noveria, the Rachni Queen mentions something about a "sour yellow note" that came out of space and warped their minds. This implication, that the Reapers started the Rachni Wars by indoctrinating the rachni and ambushing the Council races, is confirmed in the sequel if you let her live. A messenger for the Rachni Queen contacts Shepard on Illium, explicitly stating that Shepard is at war with the same enemy that enslaved the rachni and made them monsters. I don't know if this affects one's moral outlook on the genophage, but it seems pretty conclusive on whether or not the rachni queen deserves to die.
 * Look at it this way: Who are you to even judge the rachni in the first place? You weren't present when the war took place, and you don't know what happened. All the information you get is from the Council species, altered and filtered and changed over two thousand years. Do you have a right to condemn a sapient being to death based on the purported behavior of ancestors they've never known in the first place? Do you have the right to condemn her to death because she is a member of a particular species? If that's the case, shouldn't you condemn all of humanity to death because we have done some very unpleasant stuff in our time? That is the real moral choice being presented here: give the Rachni Queen a chance to make amends, or condemn her for being guilty of nothing more than being rachni?
 * Yes, I do have the right to condemn their species to extinction, I'm a Spectre, didn't you read what it said on the packet. And yeah, I'm pretty sure the galaxy already made the judgment call on exterminating the rachni after the last attempt to kill all other life in the universe. We tried to reason with them, we tried settling things peacefully, they decided that they wanted everybody dead. Attempting to wipe out all sentient life in the universe for no reason isn't a 3 strikes and you're out system. You try to kill everybody you go down hard. We killed them all then, this one is just a fluke that needs to be cleaned up.
 * The Council doesn't give you the legal right to commit genocide - they give you the legal right to work above the law as you need to. That doesn't meant that you can haphazardly ignore intrinsic sapient rights, and taking a morally questionable course of action is still morally questionable no matter how much legal protection you have. If Spectres had free pass to do whatever with no oversight, no one would have cared if Saren had wiped out Eden Prime, and the Council wouldn't have started lambasting you for genocide if you wipe out the rachni in the first place! But that's irrelevant; where was it said that the rachni were trying to wipe out all other life? They are specifically stated as launching a "war of conquest," not a "war of xenocide," and the very VI that recounts the Rachni Wars specifically states that the krogan may have gone too far in wiping them out; you yourself certainly have the option of saying this right to Avina when she tells you the story. No attempt was made to communicate with or sue for peace with the rachni by the krogan, either, after they went on the offensive. And most importantly of all, all the information you have on the rachni is filtered by two thousand years of rehashing and retelling by pro-Citadel historians. As Kaidan himself points out after Noveria, it really wasn't your place to make the call one way or the other, because humans really don't have a full picture of what's going on. In which case it once again boils down to the question of: condemn someone for being a member of a species with a bad history that itself is questionable, even though that individual is guilty of absolutely no crimes herself, or let her go despite the reputation of her species?
 * "The Council doesn't give you the legal right to commit genocide" Shyeah, right. After unleashing the Genophage on the krogan, the Council has zero moral authority to complain about "ignoring intrinsic sapient rights". Even if they could bring some sort of case against Shepard for wiping out the rachni they'd be opening themselves up to a similar case from representatives of the krogan.
 * The genophage can potentially be cured. Extinction cannot. Furthermore, the genophage was used in a time of war, whereas Shepard's incident with the individual Rachni Queen was not.
 * So genocide is okay if it's committed in time of war? Someone needs to get their priorities straightened out.
 * You Keep Using That Word. The genophage isn't genocide. If it was genocide, then all the krogan would be dead. The genophage is a population control mechanism.
 * "...all the information you have on the rachni is filtered by two thousand years of rehashing and retelling by pro-Citadel historians." As opposed to what? The word of the Rachni Queen herself?
 * Red herring. Whether or not the Rachni Queen is honest does not change the fact that the Citadel histories are, consciously or not, distorted by two thousands years of rewriting by the victors.
 * How is that a red herring? The Citadel histories may be biased, but they're no less biased than the Rachni Queen's own words. Again, the ONLY evidence we have for this alleged "bias" on the part of the Citadel is the word of the Rachni Queen herself. There is absolutely nothing to corroborate her words. If we must discount the Citadel histories because they may or may not be biased, we must also discount the promises of the Rachni Queen for exactly the same reason. And since the word of the Rachni Qqueen is the only evidence we have that the rachni are peaceful, the case for wiping out the rachni seems decidedly stronger than the case for letting them live.
 * "And since the word of the Rachni Queen is the only evidence we have that the rachni are peaceful, the case for wiping out the rachni seems decidedly stronger than the case for letting them live." How so? The only evidence we have that the rachni are violent is the feral rachni attacking you throughout the game, and we already have independent confirmation from the Russian scientist (and later, Cerberus) that the only reason those rachni were violent was because they were separated from their mother. In other words, we have no real evidence that the rachni are any more violent or destructive than any other species.
 * "How so?" We know the Rachni once waged a bloody and destructive war of aggression for nearly 300 years (the exact details of the war may be unclear but the fact that it occurred is not in dispute), which at the very least establishes a pattern of behavior. As for the Russian scientist, he only hypothesized the reason why the rachni young acted violent and aggressive. He has no concrete proof, and if he's been working in close proximity to the Rachni Queen his theory may be nothing more than a telepathic suggestion she covertly planted in his brain, so ultimately his hypothesis is questionable at best. As for Cerberus, I wouldn't trust them to tell me what color the sky was. In the end we're right back where we started. The only evidence we have that the rachni are peaceful is the personal assurances of the Rachni Queen herself. On the other hand, we have actual historical evidence that the rachni once tried to wipe out and/or conquer the entire galaxy (again, we may not know the exact details of the Rachni Wars but we do know that they occurred). Some evidence is better than no evidence, therefore in lieu of any other information killing the Rachni Queen is the correct decision.
 * So you're arguing that, based on the prior reputation of her species, an entity that is otherwise innocent of any crimes must be killed? That, essentially, you're advocating murder based on reputation instead of actual guilt or complicity in any real crime?
 * One incident is not a pattern. It's an incident. Given the debate, it's also a long shot to say that there is a 'correct' answer. Moreover, there is often times conflicting evidence or evidence ignored. The history books state that the rachni were on a war of expansion triggered by the activation of a mass relay. However, the context of this is never established and this is important to consider the missing context. Obviously, the rachni were a space-faring race and thus, by implication, capable of using mass relays. Thus, the question becomes, if they were a conquest-based race (like the krogan), why hadn't that relay been activated already and the rachni shown up as an invasion force? We can't say why or why not - they may have just been about or or they may not. This, however, with the hints of almost race-wide indoctrination suggest they could have easily been pawns as much as independent agents. And given that the Rachni Queen we meet is able to communicate, the Codex making the assertion that the rachni were unable to communicate with is very clearly wrong. While all of this does not establish the rachni as innocent, it does suggest that events were not as simple and clear cut as rachni are uniformly evil. That assertion in and of itself would also be inherently against one of the major points of the game that Wrex himself states outright - that aliens (and humans) are NOT Planets Of Hats that conform to a single attitude and behavior set.
 * There's also the point that once the last Rachni Queen is gone, they're gone for good. Once it's established that a cure for the Genophage is possible, that can be discovered again.
 * They don't even need to cure the genophage. The krogan's insane biology assured that they can and will evolve a resistance to it.
 * This is ignoring the two colonies founded by the rachni in the Styx Theta cluster, established independently, after the rachni escape from the Cerberus station. They came from Noveria, ("closer to the master control subject" means not in isolation from the Queen) and they proved quite agressive and brutal even with their mother "singing to them" not to mention founding not one but two hives on their own when there is only one Queen. Where are the eggs coming from? (Yes, there are literally eggs you can shoot in one of the Styx Theta missions) if there is no queen to lay them?
 * Wait, a second. Correct me if I'm wrong, but both the colonies established by the Cerberus escapees were both feral and uncontrolled and were in entirely separate star clusters from the ones on Noveria, which went feral from being isolated from their mother within the same facility. I don't know about you, but I think being hundreds of light years away is a little bit further from the Queen than being in the same building.
 * The recording on the Cerberus station says, and I quote "We're told these ones are fundamentally different from the specimens on Noveria, something about being raised closer the Master control subject." Which I took to mean, "raised by the Queen".
 * Also, who said the rachni required a queen to lay the eggs? If the rachni are anything like Earth insects, they would naturally grow their own queen if they were separated from their original queen.
 * Not to mention that how are the rachni supposed to tell the difference between a rogue Alliance black-ops group and ordinary Alliance troops? Even presuming that Cerberus' attempts to alter the rachni drone's brains to make them docile didn't drive them insane, after being enslaved and tortured by Cerberus its pretty understandable that the escaped rachni are killing everything they see in an Alliance uniform, because they think you're Cerberus.
 * To sum-up, killing the Rachni Queen is murder because a) the evidence that her race deserves death is of distinctly uncertain provenance (history being written by the winners, and all) b) neither the rachni nor any of her spawn were even involved in the rachni wars c) the only rachni that have even attempted to hurt a sentient being in the past millennium were ones forcibly raised under conditions that drive rachni incurably insane and d) the choice, once you've made it, is irreversible. This is as opposed to destroying the krogan cure because 1) you know damn well that the source it comes from is massively tainted with Reaper indoctrination and as such neither it nor any of its works can be safely trusted, and 2) blowing up this particular cure does nothing to prevent other people from researching a healthier krogan cure later, assuming the krogan even want to try, which so far they haven't, because they're stupid and short-sighted violence junkies.
 * There's also that if you listen very carefully to the whole rachni history from the Rachni Queen, she tells you that the Rachni Wars were started when a giant 'presence from space' began to 'sing' its 'own, discordant note', which 'hushed the songs of the rachni' and forced them to go to war. Given that rachni use the word 'sing' to refer to telepathy, the Rachni Queen is thus telling you about some giant telepathic thing from space that exerted a slow but irresistible mind control effect on the rachni queens of that day, turning them and their children into its violent genocidal pawns. Does this description sound familiar to you? It should, because it's called "Reaper indoctrination". Sovereign's been around a long time, after all.
 * The only evidence we have for any of that is the word of the Rachni Queen herself. If the queen is a sentient being then she's capable of lying to save her own skin. Furthermore, the only way the surviving Rachni Queen could possibly know that the previous generation of rachni were indoctrinated by Sovereign is if she was exposed to the indoctrination effect as well. Sure it's possible she resisted it or was protected from it in some way, but not only do we NOT know that, we have no way of finding out. No methods currently exist for measuring, detecting, or counteracting Reaper indoctrination. By releasing the Rachni Queen, Shepard could potentially be delivering a very powerful ally right into the hands of the Reapers.
 * "Furthermore, the only way the surviving Rachni Queen could possibly know that the previous generation of rachni were indoctrinated by Sovereign is if she was exposed to the indoctrination effect as well." Negatory. Rachni queens possess genetic memory from their previous mothers. This is explicitly stated in-game.
 * Genetic memory only serves to strengthen the case against the rachni. It's possible that Reaper indoctrination is now written into their genetic code. The rachni may now be hopelessly indoctrinated and impossible to reform. EDIT: Also, I double-checked and you're wrong. The Rachni Queen explicitly states that she was telepathically connected to the other rachni during the Rachni Wars ("we were only an egg, hearing mother cry in our dreams"). She may not have been able to comprehend what she was feeling or what was going on around her, but she was connected, if only on a subconscious level, to the other rachni. If the Reaper indoctrination was transferred to the entire rachni species through the rachni's telepathic link, then the current Rachni Queen was exposed to the indoctrination effect.
 * Plus, think about this: if they have genetic memory, the odds are pretty good that they might inherit old prejudices or something. Also, they might have a hatred towards us for more or less wiping out an alternate version of herself.
 * There are two facts you're missing that make it extremely improbable that indoctrination transmits down through rachni genetic memory. 1) If the Rachni Queen on Noveria was indoctrinated, there would have been no need for Benezia to mindrape it for the location of the Mu Relay: it would have provided that information to Sovereign's agent willingly. 2) If it passed on via genetic memory, the queen's 'lost children' on Noveria would never have gone feral, because they'd simply start either operating on Sovereign's last remembered command, or just sit around passively waiting for orders.
 * "If the Rachni Queen on Noveria was indoctrinated, there would have been no need for Benezia to mindrape it for the location of the Mu Relay: it would have provided that information to Sovereign's agent willingly." We don't know that. It's possible the rachni brain is so fundamentally different from an asari's that Benezia was having difficulty making sense of everything in the Queen's memory. Or perhaps the Queen was only partially indoctrinated and was still capable of some minimal resistance. We know the indoctrination effect increases over time and is permanent. So if the Queen has been indoctrinated AT ALL then she's been permanently compromised by the Reapers.
 * That egg survived for over a millenium on that ship. If she was actually able to be indoctrinated, she would have had her will crushed 100 times over in that span. Saying she was only partially indoctrinated would stretch disbelief.
 * Evidence that indoctrination is passed down genetically, please.
 * The theory that the rachni were indoctrinated is confirmed in Mass Effect 2. If you spare the rachni, there is an asari "agent" of theirs on Illium who will confirm that the rachni were being indoctrinated (the "sour yellow note") by the Reapers and that the Rachni Queen is promising that she will help Shepard fight the Reapers.
 * Exactly, and in this case rachni were definitely innocent. If Sovereign shows up, mind controls you and makes you go omnicidal maniac, he is still the one and only responsible for all the murders. On a side note I read somewhere that "genophage cure" was actually a fancy term for "cloning". Sounds like Saren actually cheated his way past the genophage to obtain a krogan army no matter what. Such a "cure" wouldn't be THAT helpful for the krogan as a whole. On a side-side note, how come that the krogan infantry are considered as such a threat in a galaxy where you can glass anything from orbit. I mean, sure they're tough guys, but even if Saren could create enough krogan warrior to literally cover a planet, the Destiny Ascension should still be able to nuke them from above. As Kirrahhe said, "crude, but efficient".
 * Citadel Conventions forbid the direct bombardment of garden worlds by warships. Once troops get on the ground, the only way to bombard them from orbit are precision sat-strikes, and even those won't work too well if you station them next to population centers the defenders aren't willing to strike or near resources/facilities they wouldn't want to damage. That was apparently why the asari and salarians were having trouble fighting the krogan during the Rebellions, because the krogan were invading their colonies and subjugating the populations, making orbital strikes impossible. Presumably, Saren would use geth fleets to support his forces from orbit and clear away ships, and have his krogan/geth troops secure things on the ground.
 * Citadel Conventions do NOT forbid direct bombardment of habitable worlds. The codex explicitly says an enemy that establishes orbital superiority "can bombard surface forces with impunity". Only the use of "large kinetic impactors" is prohibited.
 * "Large kinetic impactors" in this case probably means ship-based weapons systems. Light satellite artillery is apparently acceptable - the turians used such weapons on Shanxi, for example.
 * Large kinetic impactors mean asteroids and similar weapons. The prohibition is to prevent the destruction of the ecosystem of the garden world, as they are incredibly rare. Direct orbital bombardment from ship weapons can be small enough not to disrupt the ecosystem. You could probably wipe out entire cities and colonies without destroying the ecosphere.
 * Nope. Check the codex entry on planetary assaults. Warships cannot approach a garden planet directly because the Citadel Conventions forbid the use of ship-based mass accelerators on planetary surfaces, and defenders can use the planet as a backstop to force them to come in at a different angle.
 * The Codex entry says that they cannot attack a defending fleet directly because the sorts of weapons used against warships would destroy the ecosphere of a garden planet. In the very same codex entry, it says that once orbital superiority is established, the warships can bombard the surface with impunity. This just means they use smaller weapons for orbital bombardment than going up against armed, armored, and shielded warships.
 * Ground forces are essential, as an example, against Anti-Aircraft Guns (which in Mass Effect seems to work just as well on spacecraft) and surface to air missiles, so even if there's a planned bombardment or air combat in general, it's good to have a team on the ground. And if you've got an army of krogan as your ground forces, the odds are pretty well stacked on your side, which was probably what Saren would of thought of.
 * It's also worth pointing out that the krogan scientist who is doing the research on the genophage cure was apparently hip-deep in research on husks. That's not what you'd consider a "good sign." Also, the krogan "breeding grounds" have row after row of what looks like cloning tanks, backing up the cloning idea.
 * There are many reasons for the cloning tanks that could be true. He could clone them to see what their fetal development is like. Maybe he's cloning them so he can do some dissection and things. For all we know, they might not consider newborn, non-indoctrinated (no, I'm not talking about the Sovereign) krogans to be krogans, or they could be the only way to get krogan bodies without offending them.
 * The genophage produces sterility in that over 90% of all krogan newborns are stillborn, rather than creating a complete inability to conceive. Studying a krogan embryo during gestation would be vital to the process of developing a cure, since it's during that period that everything goes genetically pear-shaped.
 * This entire issue could have been avoided if the game had implied more strongly (it already does so with the husks, but that's not enough) that the genophage cure being developed on Virmire was either inherently flawed and useless for any purpose other than Sovereign's, or that it was impossible to recover/copy during the time limit of the base assault. This troper uses those as justifications for why the only choice is to destroy it.
 * Or maybe they left it up to the players to decide if the call was right or wrong. Some ambiguity is nice. Just a shame that games have inherent limitations on how much you can affect the story. If they actually had allowed getting the cure as a choice it would have been too big a branch, especially to be carried into two more games.
 * Couldn't this whole issue of the perhaps genocidal nature of the genophage be averted if they had created a genophage that didn't cause stillborn death, but rather just created sterility? Its not good, but its better.
 * Or perhaps even genetically modified to make the krogan more docile. Don't tell me a universe that has FTL travel is incapable of making such a genetic modification. If you are going to use the genophage to kill so many of them, why not kill them in such a way that it produces a positive change in them using artificial selection.
 * Genetically engineering the krogan to be more docile is just going to make a krogan species that is more calm, controlled, and orderly while it invades your planets and seizes your colonies. The problem isn't that the krogan are belligerent, the problem is that the krogan cannot control their population. Being unable to control their population will invariably lead to either war or overcrowding and massive death.
 * Also, why does possession of one technology of arbitrary advancement necessarily imply they're going to have arbitrary advancement in another? Just because they have access to FTL travel doesn't mean the genetic engineering is so effective that they can eliminate fundamental instincts that were bred into the krogan over millions of years of evolution. Not to mention that it was made clear from Mordin's explanations that the salarians didn't want to destroy the krogan, which making them more docile may have done. Krogan culture was kept intact, and the unique nature of the krogan were kept intact - the genophage simply controlled their population to ensure peace. Making the krogan docile would have destroyed the krogan, or at least it would have destroyed their unique abilities and advantages.
 * They were creating an extremely complicated artificial plague from scratch while under the time pressure of a galaxy-wide war. Cut the salarians some slack. The genophage had to not only A) work and work quickly but B) not kill every krogan, it must also C) transmit easily between the infected, D) not jump species (the same effect on the salarians or asari would wipe them out), and E) not change effectiveness despite enormous evolutionary pressure.
 * Being unable to control their population will invariably lead to either war or overcrowding and massive death. Apologies if I misread your argument, but if you are using this as a justification for the Genophage, then I have to vehemently disagree. Suppose the People's Republic of China, at some point, invades neighboring countries for the Lebensraum. That would in no way justify NATO using an artificial bioweapon in order to cause 99/100 of pregnancies in continental China to result in miscarriage or infant mortality; that would certainly be considered genocide. I understand the fact that the Council was facing catastrophic casualties with no end in sight, and the solution resulted in both peace and the non-extinction of the krogans, but given that the Genophage doesn't sterilize but rather chemically executes a huge amount of sentient beings is objective immoral. Now, other people here are arguing that the krogan deserved it because they were naturally belligerent, but the same thing was said about the French after the Napoleonic Wars and the Germans after the World Wars. There's enough exceptions in the Mass Effect franchise to show that the militarism was cultural, not biological. For example, the romantic krogan on Illium that is trying to get his asari ex-girlfriend to return to him.
 * Did you even read the discussion leading up to this? The line you're quoting came from a counterpoint against someone saying they should have genetically tailored the krogan to be more docile. It's not a justification for releasing the genophage at all. And regardless, krogan tendencies toward violence are biological. Mordin outright says as much, and that uplifting the krogan before they were culturally capable of coping with that violence was in error.
 * The person I quoted appears to be saying that genetically modifying the krogan to be more docile wouldn't work because the root problem is overpopulation, which is an implicit endorsement of the genophage. And regardless, krogan tendencies toward violence are biological. There is no evidence for this beyond Mordin saying so, and he was likely saying such in order to justify his own actions to himself. There are plenty of nonviolent krogan examples throughout the Mass Effect franchise.
 * The difference between the krogan and China is that China can control its population. The krogan, upon getting off of Tuchanka, keep expanding, they simply don't have room for the birthrate that evolving on Tuchanka required them to have to survive. This, combined with their enormously aggressive culture, led to the Krogan Rebellions. The root cause of that war was the krogan birthrate. If you have a better solution than the genophage I'd love to hear it.
 * Why are you so sure that the krogan cannot control their population growth? It appears that the krogan intentionally overpopulated in order to expand their influence in the galaxy prior to the Krogan Rebellions. The krogan are not mindlessly bloodlusted, as shown by the fact that they can follow orders. Or how about the fact it wasn't necessary to exterminate them after the genophage, given that they made the rational decision to surrender when they began to lose the rebellions? Take out belligerent warlords like Okeer and replace them with rational ones like Wrex and they can peacefully co-exist in the galaxy.
 * There is no evidence for this beyond Mordin saying so, and he was likely saying such in order to justify his own actions to himself. There are plenty of nonviolent krogan examples throughout the Mass Effect franchise. Bullshit. Violence is genetically bred into the krogan - that's why they have the blood rage in the first place. There are krogan who can be more rational and less aggressive, but all krogan have, at a basic level, violent and aggressive tendencies. The example you used, of the krogan poet, indicates nothing; we know almost nothing about that krogan except that he cares for his asari girlfriend and writes poetry for her. That does not preclude violent tendencies. Hell, we have a trope for violent poets. And even if nonviolent krogan exist, they are outliers. In addition, the krogan utterly refused to control their breeding habits - at least one planet in the second game is noted as having been overrun by krogan colonists in a couple of generations due to sheer birth rate. When the krogan kept claiming Citadel worlds because of overpopulation, the Citadel tried to stop them, and the krogan response was to dare the Citadel to take back those planets. In other words, when confronted with the option to control their population or go to war, the krogan chose war. As a result, krogan overpopulation and militarism led directly to the Krogan rebellions and the subsequent genophage that reduced their numbers. Thus, it is quite clear: prior to the genophage, either the krogan could not or would not control their population.
 * Yes, they refused to control their breeding habits, given that prior to the Krogan Rebellions, they were led by ultra-belligerent warlords like Okeer that wanted the krogan to rule the galaxy. They were not incapable of doing so. There is absolutely no reason to suggest their belligerency is biological and not just a result of their leaders being so. What do you suppose is going to happen when Wrex succeeds in uniting the krogans? Despite all of his tendencies that demonstrate the contrary, he's going to declare war on the Council again?
 * They were not incapable of doing so. Yes, they were. They couldn't control their birthrate because they have so many children, not out of habit, but simply because that's how their biology works. What do you suppose is going to happen when Wrex succeeds in uniting the krogans? Despite all of his tendencies that demonstrate the contrary, he's going to declare war on the Council again? Of course not. Why? Because the genophage stabilized their birthrate.

Salarian Politics

 * It says in the codex that male salarians are excluded from politics, so why is the Councilor male? Or am I missing something here?
 * How can you tell a male salarian from a female?
 * I can see your point, but I'm very sure the voice actor is a man.
 * Even if the VO is a man, that tells us nothing. For most people, the barking of a dog tells them nothing about the sex of the dog. The only reason we can tell (most) female voices versus (most) male voices is a matter of experience and familiarity.
 * IIRC, females tend to remain in salarian territory, involving themselves in inter-salarian politics. They don't get involved with external politics.
 * They never show a female salarian or turian, although it is entirely possible humans just can't tell the difference. Since they are amphibians and avians respectively, it would be weirder if the females had obvious feminine attributes.
 * Are you sure? Several salarians in the Citadel Tower are larger than normal in stature and wear hoods... what if that's not just fassion?
 * Why do the Councilors lack names, seeing as far less significant characters have them?
 * Who said they didn't? Their names are just never mentioned, and it makes more sense thematically to have them be a nameless, unified governmental body.
 * Heck, this applies to human officials too in real life. There are very long lists of directions on how to address, say, a mayor or a judge.
 * Listen to Emily Wong's news reports on the Citadel in ME 2: she will occasionally reference both "Councilor Anderson/Udina" and "Councilor Velarn." It's never specified which species Velarn is, but the context implies he's the turian representative.

Anderson In The Finale

 * How did Anderson manage to show up for the finale? They would have locked him up after what he did to release your ship. Did they release him as soon as the Normandy signalled that you had found the Conduit?
 * Put yourself in Ambassador Udina's shoes. The instant it becomes apparent that Shepard was right and he was wrong, how hosed is Udina? Udina was able to act against Shepard's authority as a Spectre only because the Council was convinced he was right and Shepard was wrong. Without that, there's nothing stopping Shepard from doing anything to Udina that he feels like, up to and including shooting him in the face. At this point, Udina has every reason to start making amends, such as, oh, releasing Shepard's old CO and best buddy from custody ASAP and dropping all charges.
 * Alternately, the Council, C-Sec, or the Systems Alliance could have ordered him released once the geth attacked and it turned out Shepard was right.

Quarian Colonization

 * Why have the quarians never attempted to settle a new planet, even if it was a marginal one? Given that humanity took over a number of previously uninhabited planets, there should have been at least one suitable planet known to the Council at the time they fled.
 * The quarians appear to be on the Citadel Council's shit list for having created the geth problem in the first place. Their applications to resettle new planets might have been denied, on the grounds that 'Look what a mess you made when we gave you your old ones.'
 * Tali mentions in an elevator conversation with Liara that much of galactic society has never stopped dumping on the quarians for having accidentally created the geth.
 * In another elevator conversation, Tali talks with Garrus about how her race couldn't re-colonize even if they wanted to, because of their fragile immune systems caused by living in space for so long.
 * In the sequel, you can find an uncharted world that was discovered by the quarians, who petitioned the Council to settle it. They started sending members of the Flotilla to live there before the request was approved, and when the Council found out, they were so infuriated that they granted colonization rights to...the elcor. With the post-script that any squatters living on the planet within a standard month would be bombed from orbit. So yes, it seems pretty likely that discrimination against quarians is "official" Council policy.
 * They also have several biological issues due to their time in space. Most significantly, their immune systems are highly compromised, making it necessary for them to wear protective clothing when outside the refuge fleet. Colonizing a planet that had its own compatible biosphere would expose them to things they could not survive. Starting a new biosphere would have involved far more material than they have at hand.
 * The problem is that they've only been on the Flotilla for a few hundred years. That's not anywhere near long enough for their compromised immune systems to have a genetic component. Their immune systems atrophy because they never use them, and then when they need them, they die. So it seems that less paranoia would be helpful: get sick, and then you won't die.
 * In the second game, a male Shepard can romance Tali, who will take every immune-system boosting precaution she is able, and still gets sick. The quarian homeworld was also equipped with a unique ecosystem that never gave the quarians much of a challenge for their immune systems, so they never developed a particularly strong system even on their own worlds. What bacteria was there tended to be beneficial, making up for the weak immune system. 300 years without anything to challenge their immune systems and nothing to help other than temporary boosts results in quarians having no natural defense against getting sick. It is implied that getting an infection from an environment suit rupture can be fatal if not quickly attended to.
 * It's explained in Mass Effect: Ascension that the quarians have a traditionalist society and they have become accustomed towards living on board the Flotilla. Due to the events in the novel, they finally go about searching for a new home.
 * Follow-up to the original question: If the quarians can't actually settle on another planet, what's stopping them from settling around one? What I mean is, why are they forced to wander the galaxy? Why not find an unclaimed solar system with sufficient resources, park their ships in orbit, and stay there?
 * That question was answered literally a line above. Its not just a case of staying on the ships, its a case of staying in one place.
 * That question is answered in Mass Effect 2. Since even after colonizing another planet, the quarians would require centuries of gene therapy to rebuild their immune systems for them to be able to live on it without the suits. The only way for any quarian living today to ever be able to live without a suit, is to retake the homeworld back from the geth, since it would take decades instead of centuries to get adapted to it.
 * So why not terraform a new planet? Before you say that's too hard for the quarians, keep in mind the team on Trebin were terraforming it by slamming ice comets into it. Hardly that difficult for the quarians. They could then slowly colonise the planet with genetically-engineered life. Hell, the Council races could do it or provide the funds/resources. I can easily see this happening during/after Mass Effect 3, as a reward for aiding in the war against the Reapers. Geth'd definitely help, too.
 * They don't have the resources. Human terraforming projects are long term and often sponsored by corporations. Quarians are basically space gypsies. They don't have any money and they don't have the spare material to build outposts on potential planets, and while it's possible they've been petitioning the Council to help, it's probably pretty low on the agenda. They definitely don't have the ability to genetically engineer an entire biosphere, assuming anyone in universe does. As to the part about the geth helping, that's assuming that the quarians would even accept their help: Tali'Zorah vas Normandy is extremely hesitant to trust a single geth representative, and only does so because of how deeply her trust for her commanding officer runs. The rest of the Flotilla don't have that luxury, especially since the last time they met, the geth were killing billions of their people.
 * Ultimately, terraforming a new planet could very well be useless. ME 2 very heavily imply that peace between geth and quarians is coming very soon, probably in no small part thanks to Shepard, and that the geth would probably happily give back their homeworld to the quarians. Hell, Legion almost says that all the quarians need to do to get back their world would be to just leave the geth the heck alone and ask politely for their homeworld. Which the geth have cleaned up in the meantime.
 * This firstly takes Legion's word entirely at face value, secondly assumes the player backed vas Qwib-Qwib, and thirdly assumes that will count for anything in the face of 300 years of quarian/geth relations.
 * The simple fact is resources and uncertainty but most importantly, infrastructure and lack of support. Inhabiting another planet is easy - heck, we can more or less do it today in regards to the moon. The problem is the quarians don't have the resources to do so (all of their resources get rolled back into the fleet) and any support they might get from other races has been burned away due to existing racism and their past habits. More over, inhabiting a planet also requires many more types of specializations than just being in a fleet. They'd have to sacrifice several ships to get power and building supplies for instance. They'd need specialists who know how to build things other than ships. Even in the case of terraforming, terraforming takes decades to happen meaning even a potential planet would not be usable for several generations to begin with... at which point, the fleet could have already taken any immediately usable resources and moved on. Which, to be fair, doesn't mean the quarians couldn't do any of these things and more... but when a population is living hand-to-foot under strict and dangerous situations constantly segregated from any widescale help, they're going to be more concerned about the here and now rather than the long term. Kinda like the krogans too.

Geth Ships

 * Seeing as the geth have more than a few varieties, are the geth dropships sentient geth or are they just standard spacecrafts?
 * If they were sentient then the geth dropship on Feros would presumably have not crashed, as an intelligent ship would have had more than enough time to fire up its antigravity drive while it was falling off the building after you sever its docking claw. An ordinarily piloted starship, on the other hand, wouldn't have anyone in the cockpit and with their hands on the controls while the ship was parked, hence, splat.
 * There's no reason to assume a sentient ship would had time to fire up its antigravity drive because we have no idea how long an antigravity drive takes to fire up. As a general rule, the larger a vehicle is the longer it takes to go from idle to fully active. A ship as large as a geth dropship would presumably take quite a while to fully activate its engines even at the best of times, nevermind when freefalling off the side of a building. And even if we assume a sentient ship would have had time to fire up its engines, it doesn't mean it would make any difference. A freefalling ship would have to a) right itself, and b) go from terminal velocity to zero within seconds (since we can't see the ground there's no telling how long they actually have). That's a lot of inertia to overcome and not a lot of time to do it in. Even if the ship successfully activated its antigravity drive it might well slam into the ground before the drive could possibly stop the fall.
 * As regards a), the ship would not need to "right itself" because if it wasn't capable of hovering while nose-down in a vertical attitude, it wouldn't have been able to land where it did in the first place. As for b), we see on Virmire during the cutscene of the geth reinforcements dropping in on the bomb site that a geth ship is capable of going from 'distant speck in the sky' to 'hovering directly over your face' in just a few seconds, meaning that it successfully executed a crash stop from greater than terminal velocity.
 * Regarding a), when the dropship was attached to the building it was pointing straight up towards the sky. When you cut it off the building it rolls in the air until it's upside down. Just because a dropship can maneuver itself to stick to the side of a building doesn't mean it can fly while upside down (and we have no in-game evidence that geth ships are capable of such a feat). As for b), you're still forgetting that we have no idea how far down the ground is on Feros. The dropships on Virmire and elsewhere quite literally have an entire sky's worth of distance to see the ground coming, rev up their engines and stop themselves. The dropship on Feros has a few seconds at most.
 * Note that the dropship rolling in the air until its upside down is by itself a huge indicator that there was no pilot on watch at that time. If there was, they would have fired the attitude jets to prevent the rollover.
 * Ashley also specifically says that the geth ship has a pilot if she's with you when you break the clamps. Or at least, she should, when I detached the clamps, I had a team of Ashley and Wrex, and she mentioned that she'd "love to see the look on their pilot's face....figuratively speaking."
 * She knows exactly as much about the geth as Shepard does, or anyone else for that matter since they are radically different from when they were last encountered. As such, her comments should not be taken as evidence one way or the other.
 * Sentience is a separate concept from anthropomorphic intelligence, and those are separate from self-preservation. None of these are necessary for any other in a synthetic, unapologetically nonhuman life form. The dropship not saving itself is no evidence that it's not an intelligent/sentient geth, just that it's not anthropomorphic - it doesn't necessarily behave like a human would. Bit of a fan-wank, maybe.
 * Mass Effect 2 revealed that the geth you see in-game are 'platforms', and that geth are AI programs that when working in concert achieve intelligence and sentience. The typical geth trooper consists of around 100 geth programs working on that platform, with more programs giving rise to greater intelligence as they work together to divide labour and solve problems. The geth are anything that can run the AI programs, be that the bidepal forms we naturally associate most with a sentient life form, or an armature, or a spaceship. Geth ships have hundreds of 'pilots', running in software. It's in the new Codex, look it up if you don't believe me (but you have to recruit Legion first).
 * But going back to assuming the ship was sentient. When you slam the door on the docking claw it would have been the equivalent of cutting off its arm. Lets see how fast you can act after a traumatizing experience like having a limb removed.
 * There's no reason a synthetic life form would have the autonomic response of meat-based humans. Pain and the desire to avoid or alleviate it override other things in Earth species because that's what worked to promote survival when life on Earth evolved. Organics that evolved differently would not have pain responses like ours - even the quarians who built the geth may not react like we do to pain, so it would have been really weird for them to program in the pain response of a species they had no contact with and which has some severe flaws . Also, a synthetic being would partition off and repair damage more easily than an organic, not necessitating the same avoidance, alleviation or trauma responses. And if the quarians did program in an anthropomorphic pain response, a self-modifying intelligent system such as the geth would also see the advantages in not being disabled by pain, and would adapt themselves accordingly to keep only the diagnostic function and not risk being turned into an idiot and dying if they stubbed their toe at an inopportune moment.

Ashley and Wrex

 * Why did Ashley
 * Well, look at it from her point of view. As far as she can see, someone is about to kill her CO. Its not like she was close enough to hear the entire conversation.
 * The question here isn't why Ashley did her job and shot him, its a question of why she delayed so long in blasting him in the first place.

Saren's Krogan

 * Did I miss a conversation? Why was Saren building a krogan army on Virmire? He has the geth to act as his private army and his plan was to release the worst killing machines ever into the galaxy. I kept waiting for a big reveal that he was secretly building a krogan army to fight the Reapers, but I never got one.
 * Presumably so that all his eggs aren't in one basket. The geth might not like it when they realise that they've been played for fools by Sovereign and Saren. Also, the krogan are significantly more dangerous than the geth, so he's upgrading as well.
 * All indications are that Saren is a very cautious person. He quite clearly doesn't trust the geth, and the krogan are consistently superior fighters than the geth, and they'd obviously be loyal to him. Plus, he was also planning to breed an army of rachni. Saren's operation is obviously quite entrenched and redundant, to ensure that someone like Shepard wouldn't obliterate all his plans with a single stroke of heroic luck. He obviously reads the Evil Overlord's List.
 * But what would he have needed them for, once he released the Reapers? Was he originally planning  before he discovered the Conduit?
 * As I understand it, the Conduit was actually a backup plan for Sovereign, or at least, the pursuit of the Conduit in the manner that occurred in game was basically a desperation move. Sovereign was very, very old, and as I saw it, very, very cautious. Its original plan probably involved dropping a veritable army of geth, krogan, rachni, and whatever else he could bring forth. When Shepard managed to actually make contact with the Beacon, however, all bets were off, and Sovereign probably commanded Saren to make a bee line for Ilos.
 * It wouldn't have surprised me that Saren would have intended to use the krogan he created at his lab as part of his assault forces on the Citadel itself. Also, don't forget that the Reapers' process of galactic purging takes place over a prolonged period of time, centuries or more, and they make use of indoctrinated slaves to support their operations. What better slaves can you ask for as auxiliaries than the krogan?
 * Remember, also, that up until a few weeks before you hit Virmire, Saren was operating completely off the radar. No one knew what he was doing, and he had all the time in the world to marshal his forces and put his plans into motion. It wasn't until Shepard started actively tracking him that there was a serious threat to his operations. The timetable very, very quickly changed once he was exposed and Shepard started hunting him.
 * Also, remember that
 * In addition, one must differentiate between the plans of Saren and the plans of Sovereign.  In the end he may just have been planning to use the geth, krogan and rachni to wipe each other out or keep each group under control. Consider this, the krogan were needed to defeat the rachni, a genocidal plague was needed to defeat the krogan, nobody was able to defeat the geth.
 * The Conduit was indeed plan B. To get to Illos, Saren would have to find the Mu Relay, which as far as he knew would take decades if not centuries of combing through space. It was chance that the rachni knew where it was, and that they were revived, and that he gained an ally powerful enough to extract the info (he probably never expected to have a Matriarch on his side).
 * It is, fairly vaguely, implied that the Rachni War may have been caused by Sovereign. Since the Protheans were the only galactic-scale civilization when they were wiped out, and that the salarians had recently arrived on the Citadel, Sovereign may have thought that was the right time to begin the extinction. This would be when it found out the Keepers had been altered. So instead of rushing blindly into a likely fortified space station, Sovereign indoctrinated the rachni, as described as a "sour, yellow song" by the Queen. It's really vague (probably intentionally) as to when Sovereign decided it was time for a little Mecha-Cthulhu reunion, and this puts a new twist on sparing the Queen on Noveria.
 * Saren explains it, in part, himself. By making organics useful, he hopes that that will be enough to save them. Thus by developing an army that is mostly organic, he can demonstrate that very point.
 * Kind of suggested at in ME 2.

Volus and Elcor, Relationship with Council

 * [Seems to be missing initial Just Bugged Me bulletpoint]
 * The whole point behind the volus and the elcor sharing an embassy is that they've been getting shafted for so long by the Council. As for the elcor, you don't see them do much, but Xeltan does move his forearms around when you talk with him before bringing Septimus' OSD to him. When he does this, you can see that his forearms definitely have fingers on them.
 * Yeah, but the Codex explicitly states that all four limbs are legs, and their balance pretty clearly depends on staying on all fours. Maybe they could manage it in lower-gravity environments like the Citadel, but how would they have developed such technology on their own homeworld, where they can't afford to lose their balance?
 * Very carefully. That's the elcor's hat.
 * Indeed. There is no reason why they couldn't stand on three limbs while manipulating objects with fourth. Although it would require more than one individual for any complex work. Of course that would increase cooperation considerably.
 * Which makes sense, considering the elcor's communal and conservative nature. The elcor have a very, very strong biological directive to be team-players and are fundamentally cautious creatures. Having this reinforced by requiring extensive teamwork to do complex physical tasks just applies a powerful psychological imperative to work with others. Hence why all the elcor you meet are pretty nice guys.
 * There's also no mention of elcor biotics at all. I'd imagine that they hold a special place in elcor society as artisans, craftsmen (craftselcor?), and heavy lifters, since they could manipulate more objects with more precision than your typical elcor could.
 * Just an idea: maybe they use their trunks?
 * "There is no reason why they couldn't stand on three limbs while manipulating objects with fourth." For that matter, there's no reason the elcor couldn't just sit down while they work, thus giving them the use of both hands at once.

Destruction of Virmire

 * When you destroy the base where Saren is making his genophage cure, why not just drop the bomb from the Normandy?
 * They mention the reason for this at the salarians' camp, the base is too fortified to be destroyed by a bomb from the outside, also the AA towers were keeping the Normandy on the ground anyway, so they'd have to run in, disable the AA, pick everybody up and then drop the bomb, guess they just figured it'd be easier to plant the bomb while destroying the AA guns.

Human Council Membership

 * The very fact that humans are even being considered for a membership on the Council just bugs me. Judging by some conversations you can listen in, not only is this considered a likely scenario, people seem to have come to terms with that. Even some volus, who were getting the shaft for over a thousand years. It's been what, 26 years since first contact? And that one turned into a war? And 19 years since humans have even been granted an embassy and they're already going "Waahhh, we want to get say in galactic matters. Give us Council membership NOW!" How come they don't get kicked off Citadel Station and told to come back when they grow the hell up?
 * I think the turians were added to the Council pretty much as soon as they met the other two races, thanks to their help in the war against the krogans, so there is precedence. The other races probably get the shaft because they kind of suck.
 * Plus, the Council's based on military acheivement. Doing well in a war of first contact would probably HELP human's advancement into the big chairs.
 * The humans being considered to be members of the Council is kind of the whole point. Humans do some stuff that shakes up the Council races as well; they've got an enormous fleet for their relatively young age, they successfully fended off a massive pirate/slaver assault on one of their main colonies and retaliated with such force that they made the batarians withdraw from the Citadel, and humans innovated tactics and weapons that are completely new to the Council species, like dedicated attack carriers, and one of the best arms and armor manufacturers in Citadel space is, yep, human. Unlike the volus or the hanar, whose military or political accomplishments are relatively lackluster, the humans definitely have major potential that outstrips that of other, more staid and peaceful species.
 * I dunno. The volus should have more clout considering they standardized and run the galactic economy. It's probably because of their pact with the turians that keeps them off the Council rather than their importance.
 * This is pretty much the main reason right here. Really, the only reasons the Council is not composed entirely of asari was the fact that not sharing the Citadel with the salarians would have sparked a war; same deal with the turians. The First Contact War proved that the humans had enough military might to take on the turians, and they were inducted into galactic society far more quickly than they would have been otherwise, simply to avoid starting a bloody inter-species war that would have both sides bitter and hateful towards one another for centuries.
 * The Codex provides some potential insight. In the Turian Hierarchy, which the volus are a part of, the social position of civilians (who lack citizenship) is encompassed by children and client races. It's only after military service (or flunking out of that for members of client races) are civilians given citizenship and the rights thereof. Thus, as far as the turians are concerned, the volus are basically equivalent to children and have been for thousands of years. The volus asking about it all the time probably reaffirms the turian belief (and it's not like the volus have any say in turian matters anyway lacking citizenship); the volus ambassador is probably mostly correct in that the only reason the volus have an embassy to begin with is their economic contribution/to shut them up not due to any real political sway. And the asari and salarians annoying the turians by giving the turians' children a chair would probably cause more political grief than anything else, at least at first. The volus are just in a very bad situation - they don't have a military so military prowess is out, they don't have political sway so that's out, and while they could hold the economy hostage, without any of the above two, that'd be asking for a military response.
 * If TIM in Mass Effect 2 is as influential as Cerberus claims him to be, it's possible he was working his ass off to get humanity a Council seat before and during the events of ME 1, and succeeding.
 * Avina actually specifically explains why the volus, elcor and others don't have seats on the Council. Simply put, they don't have the resources to meet the obligations being on the Council brings, especially the military obligations. The humans are newcomers, but already, we can meet those obligations.
 * I'd guess that the fact that the volus are part of the Turian Hierarchy hurts their chances. The council probably thinks "You are already represented by the Turian counselor and there is no reason why the Turian Hierarchy couldn't chose a volus diplomat."

English Citadel Markings

 * Why the heck are there giant human language digits marked all over the Citadel, in such a fashion as to suggest they have been there for a long time (or even belong there)? For instance, there is a giant "09" written on the side of the Citadel Tower. If this was written there just for the humans, what the heck does 09 mean? It also appears in other places. If it was written there just for humans... why??
 * The Keepers did it. Their entire job is to make sure the Citadel is usable for those species that occupy it, and humans have become very important lately, so they repainted the Citadel.
 * You're also being rather presumptuous. You don't know that it's stylized font of "09." For all you know it's Reaper or Prothean writing that just happens to look like "09." The simplest answer, though, is that it was painted there later on.
 * While there is a common trade-language, almost everyone in the Mass Effect universe carries what we would term a "Universal Translator". It's made clear in the novels and DLC, if I recall correctly. Hence, why most of the alien races speak in pleasant North-American dialects. It's not too hard to imagine that there also exists a method to translate alien writing (whether via microchips in the brain, contact lenses, a helmet's HUD, what have you).
 * So each person has a mini Tardis on them somewhere?
 * Given that the hanar communicate by glowing, which gets translated correctly, it's not hard to imagine that the standard translation unit handles text just fine.
 * The way I see it, the Protheans used a language with characters that look the same as the Latin Alphabet, which is why one of the towers on Ilos has what looks to be, but can't possibly be "Bioware" writen on the side.
 * Why can't it be? Maybe Bioware was a Prothean organization or something. It's possible that the real Bioware never existed in the ME-verse (and if they did, they presumably didn't make a game named Mass Effect).
 * Perhaps Bioware does exist, but in 'future' form, like how Karpyshyn in-universe is contemporary and writes historical fiction. Would be a good easter egg for Mass Effect 3.

Bring Down the Sky

 * In Bring Down The Sky's Paragon choice, why on earth can't Shepard just call up the Normandy the second the bad guy's out of the room and tell Joker to turn the escaping ship into a debris field?
 * Presumably, in the time it would take Joker to destroy his ship, he would blow the asteroid out of spite.
 * Why the hell does Kate Bowman refuse to say anything to Balak? It's not like she knows anything about you anyway. She got her brother killed for nothing. I suppose there's the idea of simply not cooperating with terrorists at all, but it seems to me that saying "I don't know" would work better than just turning around.
 * Why would you assume that "I don't know" would be a totally 100% satisfactory answer to an insane, genocide-bent zealot? "You don't know? Okay, you're all free to go."
 * It could go one of two ways. Either Balak kills Aaron anyway, or he keeps him as another hostage. There's a possibility - slim, but there - that telling Balak something will get Aaron spared. Saying nothing is guaranteed to get him killed. I've just never understood why she would turn her back rather than just say she has no idea, which is actually the truth anyway. She doesn't even have to lie.
 * She doesn't know who you are, but she does know where you are: you're shutting off the fusion torches per Kate's instructions. Remember that Balak isn't sure what's going on until you actually hit the main facility - otherwise he would've sent his entire force to ambush you at the third torch instead of his lieutenant and a handful of troops.

Earthborn

 * In the side quest for the Earthborn background, one of your old gang tries to blackmail you. The Intimidate response, netting you Renegade points, is to tell him that no one will care. The neutral response, affecting your Karma Meter not a bit? Gun him down in cold blood. Seriously, what?
 * Pay Evil Unto Evil
 * Incorrect. Having just done that mission, I can confirm that you get the exact same number of Renegade points for killing Finch in cold blood that you get for intimidating him.
 * This troper can confirm this whole system in wonky. When you're storming Fist's place you discover some innocent guys in the back. You have the option of killing them, intimidating them or charming them. If you choose to kill them, you get 2 Renegade points. If you intimidate them, which doesn't kill them or harm them in any way, you get 8 Renegade points. lolwut.
 * This is because your Paragon and Renegade ratings aren't specifically about measuring your character's morality; instead, they measure Shepard's reputation. Scaring the pants off someone and letting them live to spread the tale has more effect on your rep than just killing them (particularly since generally to get to the point where Shepard has a high enough Intimidation rating to take those options, he or she will have first gunned down enough people to back up the rep).
 * That does fit with many of the events shown in the game, as well. For example, on Noveria, if you use the Charm method to talk Anoleis' goons into leaving without a fight, you get Paragon points. If you use Intimidate, you get Renegade points. They both have the same effect, but one method involves you being reasonable and patient, while the other involves threats. The obvious reason why this works - and why extra points in Renegade and Paragon affect Intimidate and Charm options - is that the meters in question reflect reputation, not actual actions.
 * Actually, that is justified. Whether or not they're warehouse workers, they're still criminals, and are still criminals who are pointing guns at you. Talk to any real-life soldier or police officer, and they'll tell you that in that exact situation, an enemy combatant who is armed and pointing a weapon at you - especially after shots have been fired - is considered a legitimate target. In fact, realistically speaking, Shepard and his team shouldn't have even stopped when confronting those workers. Since they were armed employees of Fist and pointing weapons at them, Shepard should have just killed them. That's why killing them generates fewer Renegade points - killing them is, by all measure, perfectly legitimate.
 * Who's the criminals you're talking about in the second sentence exactly? The thugs that shoot at you immediately? Because the example is confusing me.
 * The warehouse workers are criminals. At least, it can be assumed that they are, since they work for Fist and are willing to point guns at people for him.
 * Or, if not "legitimate" from an ethical point of view, at least not the actions of a renegade, hence the name. You get Paragon points for being "good cop" like a smarter version of Dudley Do-Right and Renegade points for being a "bad cop," in the sense that, say, Dirty Harry is. Shooting someone who's already pointing a gun at you is neither "good cop" nor "bad cop," because either or both of them could plausibly do it. It's "neutral cop."

Nonuel, Plutus, Hades Gamma Cluster

 * On the Planet Nonuel in the Plutus system, Hades Gamma Cluster, there's a spot on the map marked as "Warlord's Outpost" I mark it on my map, drive there with the Mako, I see a building, I'm thinking "great a cool mission where I get to kick some Warlord's ass to next tuesday" But when I get out of the Mako, I find there's no way to get in. I look all around the building, trying for a hidden entrance. Nothing. I spend so much time looking I don't even notice the level 2 heat hazard and die. Why can't I get in? Better yet, why put this in the game at all? Is it just there to annoy people like me?
 * That planet and another one appear when you have sufficient Paragon/Renegade points to trigger one of two special missions Hackett will give you relating to your alignment. Nonuel is the Renegade one, where you have to negotiate with the warlords, while the other one is hostage-rescue mission where terrorists are using drugged scientitsts as human shields. If you didn't get the warlord negotiation mission, you'll only be able to go to the planet, not actually engage in any sidequests.

Talking to Unresponsive Aliens

 * There are a number of different creatures, basically local wildlife that inhabit some of the more Earth-like worlds you do your countless side quests on. One of the creatures you run into is a race of centaurs, basically deer with hands. You walk up to them and the "push A to talk" screen pops up. You press it nothing happens, so Shepard is just a crazy person who likes to talk to random alien creatures.
 * ... That "centaur" wasn't the Shifty Looking Cow, was it?
 * Well you never can tell what's sentient.
 * The real answer is they were probably supposed to be sentient yet primitive, and part of a sidequest. But that got cut at the last second since Microsoft wanted the game out for Thanksgiving, but it was a shoddy cut, so the press A to talk sign is still there, but they don't talk. Also note that one of them will steal some of your credits if you don't pay attention.
 * And there's also that side quest where you have to search some monkey colonies.
 * The animals are just dicks. Shepard's trying to be nice, and they ignore him.

Mako on Fire

 * How does the Mako catch fire on planets with no oxygen?
 * Other combustible materials that likely have their own oxidizers. You don't need oxygen in the air to have fire on worlds without it if the materials that are on fire have their own oxidizers, which is why gunpowder in real life can be lit off in a vaccuum.
 * There's also the Mako's own oxygen supplies. If damage to the Mako springs any leaks...

Saren Looking for the Conduit

 * The very first information Shepard and company get about what Saren is up to confirms that he's looking for the Conduit in order to bring back the Reapers, and most of the plot involves both Saren and Shepard trying to find the Conduit. This stops making sense when we find out that the only thing the Conduit does is give Saren access to the Citadel - which, as a Spectre, he already had right up until Shepard got him fired and sent him on the lam. Had Saren not attacked Eden Prime and gotten Shepard on his case, he wouldn't have needed a back door onto the Citadel in the first place.
 * Sovereign was being cautious again. Saren would have had to have done it alone or with a small group of others, and just think what would happen if he suddenly started hacking into Citadel Control. C-Sec would be on him in an instant, not to mention the Council's Honour Guard. The Conduit was instead a way to get a whole army into the place undetected, to clear his way to the Council Chamber.
 * Saren has access to the Citadel, but the geth do not. And remember, the control room for the Citadel is the Council chamber itself, which is the single most well-protected room in the entire Citadel. The moment Saren walks up to the middle of the chamber and starts fiddling around with something, folks are going to start asking questions, and if/when the geth fleet and a giant Reaper ship pop out of the nearest relay, those questions are very quickly going to become bullets. In order to take the Council chamber, Saren will need backup to both control it and keep C-Sec busy long enough for him to take control and let Sovereign do his business. Otherwise exactly the same thing would have happened as when Shepard attacked, except it would have been an army of C-Sec special response troops.
 * "Saren has access to the Citadel, but the geth do not." Exactly. The point of the Conduit was only to get enough geth into the Citadel to seize control of the station and release the rest of the Reapers.

Sensors

 * How is it that the Normandy's sensors can detect the mummified corpse of a salarian scavenger from orbit, but can't detect half a dozen geth Armatures plus backup hiding in the sand?
 * Geth can shut down their eezo cores, which makes them practically invisible to scanners. That was how Matriarch Benezia was able to smuggle an army of them in past Noveria's ultra-paranoid security measures. Also, in most of their ambushes, the geth actually drop in from outside the battle zone instead of hide in the sand. Normandy's own sensors are actually quite capable of picking up geth anyway, at least when they're active, as shown on Feros.
 * Also, I don't think the Normandy's sensors ever specifically detected a salarian corpse. Just an "anomaly". And as I recall, all the geth ambushes originally showed up as "anomalies" on the Normandy's sensors as well.
 * Further to the anomaly phenomenon, case in point: Xavin. There is a dead miner outside his vehicle at the south end of the map, and a Geth ambush at the north. Both are classified as "anomaly". Both have locator beacons on site. There are other salarian corpses you can find base on anomalous readings from the Normandy, which includes crashed escape pods and emergency locator beacons. In the case of the geth, they're luring you to their kill zone with Alliance emergency beacons which are supposed to be visible from orbit.

Ilos

 * If all records of Ilos were destroyed, how come Liara's heard of it?
 * Same way Sovereign knew enough to send Saren looking for it in the first place. The destruction of records was only 99+% complete... enough to entirely remove it from the Prothean census rolls, and keep the Reaper invasion of the day from realizing its significance or existence, but not enough to keep people from figuring things out in 20/20 hindsight if they spent decades of painstaking archaeological research on other Prothean worlds assembling all sorts of tiny, otherwise meaningless secondary indicators. And note that Liara knew nothing except that a Prothean world named 'Ilos' once existed, and illustrations of some of its scenery at ground level — which she could have gotten from as little as one remnant Prothean postcard found in a ruin somewhere. The significance of Ilos and the existence of the Conduit is knowledge obtainable only from the Prothean beacons... which were transmissions deliberately set up after the apocalypse by the survivors of Ilos, to hopefully contact other Prothean survivors.
 * The Reapers not only had indoctrinated Protheans who would presumably have told them everything they knew, they also spent three centuries trying to find every last shred of Prothean civilization and destroy it. If there was any evidence at all that Ilos existed (beyond the secret records that were destroyed during the attack on the Citadel), they would've found it. And yet in the present, knowledge of its existence is widespread enough that Tali mentions that the quarians once tried to find it and the codex mentions that several universities have tried to mount expeditions to it.
 * Uh, look at the surface of Ilos. The little fact that there are no living Protheans on the surface is a pretty darn good indicator that the Reapers did find Ilos and killed everyone on the surface. They just never found the Protheans' hidden bunker. Ilos is probably actually very well-known, its just that no one knows how to get to it, nor do they know that the Conduit is there.
 * Also, Vigil specifies that the records destroyed related to his facility in particular, not to Ilos as a whole.

Human Space Exploration

 * This troper has a bit of a problem suspending disbelief over the timeline of human space exploration as outlined in the Codex. Prothean ruins were found on Mars in 2148, and by 2157 - just nine years - humanity had deciphered the data, unlocked the Charon Mass Relay, colonized at least one new world (Shanxi), and developed an interstellar fleet capable of standing up to the most militaristic Council race (who have supposedly been a spacefaring species for at least a few thousand years)? All that advancement in just NINE years? Sure, it needs to be made clear that the Council feels threatened by humanity's rapid expansion, but this incredibly abrupt timeline seems excessive.
 * That's the whole point. There's a reason the Citadel species are quietly terrified of humans. Its also worth pointing out that the Alliance fleet didn't exactly "stand up to" the turians during the First Contact War; their fleet was actually quite small, and the only reason they retook the planet was because of a relatively small turian presence. According to Mass Effect: Revelation, human:turian losses favored the turians. The turians themselves were gearing up for a full-scale invasion in which the human fleets would have been utterly obliterated if the Council hadn't stepped in to negotiate a cease-fire.
 * Uhh, no. The loss ratio actually favoured the humans - albeit by a tiny margin. Just over 600 humans killed, with slightly more turian casualties.
 * The Prothean cache on Mars may have been found some time before 2148. There is a mention of this somewhere in The Codex.
 * Uh, no. I don't recall any mention of that in the Codex. The south pole of Mars had developed a "Bermuda Triangle" reputation, but that's it.
 * Humanity was already pretty far ahead by 2148. Gagarin Station (Jump Zero) at the outer edge of the Solar System - over twelve billion kilometres from Earth - was completed before the Mars ruins were discovered. Humans began mining Helium-3 from Saturn (one billion kilometres from Earth) in 2137. We didn't know what Element Zero was, but we weren't living in grass huts.
 * Also, look at the introduction of the USA in WW 2 and the results. It took a very short time for the country to switch into military production mode and the development of things like the atomic bomb. Now translate that into a global scale with a singular purpose (HSA not the Earth nations) and it makes a little more sense.
 * The use of the United States as an analogy is pretty apt. In the Codex the Alliance is actually referred to as a "sleeping giant" and the Treaty of Farixen, which regulates dreadnought numbers has many similarites with the Washington Naval Treaty. Notably, many nations got around the constraints of the Treaty by building aircraft carriers, which were lighter than battleships. In-universe, the Alliance got around the Treaty of Farixen by building carriers; it's safe to assume that the Treaty only defines a "dreadnought" by firepower, not mass.
 * Don't forget that the eezo generator was on and generating a mass effect field. Any physicist would take one look at that and weep over the implications. Presumably every human pysicist and engineer was working on this 'round the clock until they cracked it.
 * Worth pointing out too that the whole idea of the mass relay network is that they are used by everyone. Chances are high that not only only are they there, but they're also designed to be easy to understand and probably have a copy of "Baby's First Interstellar Navigation System" lying on a desk somewhere.
 * 26 years passed between the First Contact War and Mass Effect 1. Most of the characters – including Shepard – were born before this point. I find it hard to believe that humans have reached their apparent level of integration into the galactic community in a single generation. Things like John Whitson, that kid who grew up on Omega – his parents must have moved there less than a decade after the end of the First Contact War. It all points to humans having been around longer than the timeline says they were. If I were Bio Ware, I would have simply pushed the events of Mass Effect 1 up by about 20 years or so, giving us another generation to integrate.
 * They haven't perfectly integrated -- that's the point. They're still being integrated, and the process isn't going smoothly by any means. The human "hat" in this setting is expansionism, and the other Citadel species are stunned by humanity's rapid advance in galactic politics.

Tali and the Geth
The terminal on Feros doesn't contain orders. All it contains is unspecified information relating to a geth invasion of the Armstrong cluster. There's no evidence those geth invading the Armstrong cluster were under Saren's control.
 * According to Tali, to get any meaningful information on the geth you'd have to find a group of independent geth, who aren't under Saren's control. I stumbled across the geth in the Armstrong Cluster by myself, so at first I didn't see anything wrong, but then I discovered that there is a geth terminal on Virmire that contains orders for the Armstrong geth from Saren. How is the data from that geth outpost useful to the Tali for her pilgrimage if they are obviously under Saren/Sovereign's control?
 * I'll need to double check, but I'm pretty certain the terminal only contained coded transmissions, not necessarily orders. If that's the case, the two groups were in contact with one another, but its not evidence that the Armstrong Nebula units were under Saren/Sovereign's control.
 * And, in ME 2 we find out that the geth were divided into two factions, and that the 'heretic' faction (the one allied with Sovereign) was spying on the other faction. Which entirely explains both the geth in the Armstrong cluster not being affiliated with Sovereign, and Sovereign's geth knowing about the troop movements. Of course, this also means our entire 'massacre the Armstrong Cluster geth presence' mission was us blowing the crap out of hundreds of Legion's old friends without provocation, when the true geth were just trying to live their own lives and only shooting at people who were clearly there to murder them, which makes this troper feel kinda guilty now.
 * The geth in the Armstrong Cluster were using Husks, and Legion says explicitly that it is the first meeting of Shepard-Commander and true geth.
 * Wait, what? I could understand that being Shep's first contact with true geth (I don't remember Legion mentioning this, but it's possible), but why were they using husks, which are clearly stated in ME 2 to be Reaper tech? Legion distinctively states that the true geth did not accept help from Sovereign.

Vigil and Reaper Resource Management
How about this one: We know from Vigil that the Reapers strip the galaxy bare of all technology and natural resources once they've conquered it and before they retreat back into dark space. If so, where the hell does the next set of intelligent species get the resources to, you know, advance into space to the Reapers' desired tech level?
 * Vigil's a VI that's been stuck in a bunker for a fifty thousand years with no access to the outside world and no maintenance. Do you really trust him to know everything about the galaxy after having degraded that long? He himself says that some of the information he provided relating to the Reapers' actions was conjecture, and it's quite clear that he was mistaken about that part when you consider other species have arisen and that natural resources haven't been consumed.
 * I always took it to mean that species from certain planets would rise up, discover space flight, open up all the mass relays etc etc, and eventually draw the Reaper's eye, while all the species that were still in their infant stages were left untouched. Note how so many of the Mass Relays have yet to be activated, meaning there's a whole host of species that would probably be left alone when the Reapers came. 50,000 years ago when the Protheans were at their height, we were in the middle of the Stone Age (or not. Doesn't matter ultimately, you know what I mean).
 * While the Reapers' need to strip-mine the technology makes sense in this context (they don't want the next generation to discover what happened), given what the player discovers in Mass Effect 2, "natural" resources pretty clearly means the species that make up galactic civilization themselves. Kudos to Bioware for being vague enough in the original to pull something like that for the sequel.

Shepard's Backstory

 * The way some of the background story choices for Shepard sync up have Unfortunate Implications. If you pick the Spacer/War Hero background, it looks like you're trying to out do your parents. If you pick the Colonist/Ruthless background you look like an axe crazy bastard so hell bent on revenge you're willing to get your entire team slaughtered to get back at the guys who attacked your home. And if you take the Paragon path after picking the Ruthless origin story, it seems like you're spending the whole game in Wangsty repentance.
 * .....and? What's the problem here? You get a summary of those background choices at the beginning of the game when you create a character, so you're the one who picks this character's background in the first place.
 * "If you pick the Spacer/War Hero background, it looks like you're trying to out do your parents." What's wrong with that? The desire to achieve more than your parents did or could seems like a perfectly normal motivation for any person to have.
 * None of them seem that unfortunate to me. If you pick Colonist/War Hero (as I did) it could look like Shepard's War Hero defense at Elysium was motivated by a "Never Again" determination in the face of the batarians. Or it could be triggering old, bad memories and have driven Shepard to a near fanatical zeal in his/her duties. Neither is inappropriate.
 * It's called Roleplaying. Sure Spacer/War Hero Shepard could be an arrogant overachiever looking to outdo their parents, but they could equally be someone who got pushed into the Military by parental peer pressure only to find they had a real talent for it, or someone who grew up hearing about generations of military tradition and wanting to honor that. It all depends on the image the player has in their head.
 * I don't agree with a Paragon run with a Ruthless background being "Wangsty repentance." Wangst usually means your character is sad to an overly exaggerated form. The Paragon answer to Coporal Jenkin's comment about how'd you be a good Spectre due to Torfan was just a simple "I didn't enjoy it, but I did what I had to do." Which means you've accepted what you've done, you sure as hell didn't like it, but you know it was the only way to make Torfan a success. When you talk to Ashley or Kaidan after Virmire and they ask you how you dealt with Torfan you can just say "I promised I would do better" and keep it at that. A Paragon run with that background is basically you living up to that promise by actually acting on it. If it was "Wangsty" then you'd just sitting there whining about Torfan without doing anything to make up for it. (Not to mention going on and on about it to everyone's annoyance as well.)
 * For me, a Colonist/Ruthless background but Paragon play (basically randomly chosen for my first playthrough), really came together after doing the "I remember me" quest. That is why 3/4 of Shepard's squad died on Torfan, and why she executed unarmed prisoners. The marines who died on Torfan knew the score, and knew the risks. The lives of dozens of marines, who had reasonably normal childhoods and who went into combat willingly, would be a fair trade to keep more children from ending up like Talitha.
 * And inversely, being a Colonist War Hero and going Renegade is being a ruthless Spectre who with little in the way of bureaucratic oversight will be able to go all out against slavers. But what doesn't make sense is a Renegade Spacer/War Hero.
 * Why would that not make sense? Shepard would have been raised by a military family - which can translate to, "in a home environment heavy on rules and light on overt shows of affection," depending on the family - and enlisted to do his/her duty. The Blitz comes along, and Shepard does his/her duty, in the process proving s/he is a supreme badass.
 * Also, consider that there were a large number of aliens amongst the ones who attacked Elysium. Many of the Renegade decisions have a highly human-centric bent, as opposed to calling for cooperation with other races. Maybe he/she saw the multi-attack species on Elysium as evidence that maybe humans should stick together and not worry so much about cooperation. It's possible that Shepard blamed the alien influence on the decision to attack and therefore would carry a grudge against non-humans - not a highly rational response, but considering the circumstances it's not impossible.
 * Now a Paragon Earthborn/Ruthless, now that is a huge personality contrast.
 * Well, there is the repentance route that the OP mentioned. Shepard is very much aware that because of him/her, a lot of good people died. Maybe it was the only thing he/she could do then, the only option that Shepard could see at that time because of how life on Earth shaped him or her. But maybe that event inspired him/her to make sure that there will never be another situation like that again, and to seek different solutions when possible. Paragon Shepard isn't a cowardly wuss, after all - just a person who picks battles carefully and avoids them when they can be avoided.
 * As for Earthborn: Shep has been on Earth, he/she has seen what a rotten cesspool it can be and thu has no romantic pro-Earth/human ideals, so they instead push for interspecies cooperation. As for Ruthless, repentance as mentioned above is a powerful force, though it may simply be that Shepard has personally seen how costly that kind of attitude can be - maybe a different route is actually more pragmatic (particularly for Paragades).


 * Why does no one ever comment on Shepard being a biotic? It's repeatedly mentioned that humans are leery of biotics. Kaidan being a biotic was the whole schtick of his character. There are at least two human biotic cults. I realise that not every playable class has biotic abilities, but it's wierd that this is the only custom feature that no one notices, when it's such a big deal to the rest of the galaxy.
 * Shepard's awesome outshines any mere ability to throw a tank around with your mind.
 * The real Fridge Logic sets in when you talk to Kaidan about his past. Since the Shep is always at least as old as Kaidan, a biotic Sheperd should have gone to brain camp at about the same time, and should probable already know all about it.
 * Kaidan was 17 and Shepard was 14 when B Aat was shut down. It's not made clear, but it seems Kaidan was somewhere older than 14 when he was sent to Brain Camp.
 * All three of the Shepard backgrounds present workable possibilities for keeping Shepard out of B Aat. If Earthborn, Shepard was just a random kid in a random gang on Earth who would have been hard to find. If a Spacer, s/he's the child of Alliance military, who might have refused to let their child be taken to B Aat. If a Colonist, Mindior is remote and far away and would be hard for them to reel Shepard in. It's clear Shepard joined when s/he was older, and probably received training in biotics after B Aat was shut down.
 * Ask Kaidan why he didn't get the surgery to replace his L2 implant with an L3 retrofit that would cure his migraines. He'll explain that he's essentially embraced what he is, problems and all, and is happy with it, while switching to an L3 would lesson his biotics because L3s are usually weaker than L2s. If Shepard is a biotic, Kaidan has an additional line where he mentions that Shepard is a rare L3 who can match an L2 and an asari commando. It's not much, but it's a mention, at least.

Temperature Hazards
After further review and a quick reading of Bad Astronomy, it appears you are correct.
 * Setting aside that information labeled simply 'surface temperature' almost certainly broaches on useless (I guess it could be mean current surface temperature, but that only really tells you what the temperate zones are like), isn't anyone else annoyed that there's a functional cold hazard on Noveria? Readings from orbit indicate remarkably Earth-like conditions (similar atmospheric pressure/gravity), and surface temperature reads -1 C. That's scarcely cold enough to freeze water, and warm blooded characters in your party wouldn't be threatened by a temperature like that. Hell, in a decent jacket, they might even be comfortable. What's the game do? It not-so-slowly kills you if your effectively-a-spacesuit-wearing Space Marine stands out in it for more than a minute or so. You are, of course, free to lollygag about on planets an order of magnitude (if not two) colder without any time limit or risk of damage from the environment.
 * There is a hideous blizzard going on by the time you get outside. The -1 C temperature reading is apparently before the weather turned to crap, or else was taken from another location planetside.
 * Because as we all know, when you take the temperature reading from one spot on a planet, it will be the exact same everywhere on the entire planet, without variation. Oh, wait.
 * The fast moving and dense atmosphere of Novera could carry away a lot more heat then, say, the near vacuum of Luna. Even if Luna in the shade is -150 C and Noveria's only -20 in the storm.
 * You can see stars from Luna. The light side of Luna. The reason you never see stars in any of the Apollo mission photographs is because they're all taken on the light side of Luna, and you can't see stars in them for the same reason you can't see stars during the day on Earth: there's a humongous light source way too close for you to see, well, anything else.
 * Not so. You can't see stars on light side Earth because the atmosphere scatters enough sunlight to wash out the relatively dim stars and even the rather bright moon. Without an atmosphere in the way you can cover the sun up with your thumb and see every other star in the sky just fine.
 * Also, don't forget the power of wind chill. In a cold environment even a mild wind speed can dramatically increase the effects of the cold.

The First Contact War

 * The First Contact War - beginning to end. The favored strategies of various species is All There In The Manual; salarians spy on everybody then make preemptive strikes, turians hold back until peace is impossible then throw everything at the target, asari respond to declared threats with precision attacks. The only guys who "shoot first and ask questions later" are humans. Yet the turians supposedly found a few primitive ships screwing around with a mass relay and decided to just Kill Em All? WTF really happened at Relay 314?
 * Kill Em All mode wasn't applied. The turians encountered and destroyed the human ships opening the Relay, because that is automatically applied to anyone who is opening Mass Relays without scouting the other side first, in order to prevent another Rachni War from breaking out. The humans retaliated on the turian ships, and the local turian forces launched a counterattack on Shanxi. The humans geared up for a counterattack and retook Shanxi. The First Contact War was little more than a unexpected border skirmish anyway, and only involved the Turian Hierarchy's local military forces in the area, not the entire combined armed forces of the Citadel. Once the turians began mobilizing for a serious war, the Council took notice and negotiated a ceasefire. The reason the Council's various species didn't use their particular strategic strengths was because the incident happened and was resolved so quickly, and it only involved local turian forces instead of the entire Hierarchy military. Its kind of the equivilant of a US Navy patrol group engaging in a sudden, minor skirmish as opposed to a full-scale invasion with the entire extended US military.
 * It's still an uncharacteristic overreaction - the in-game argument is that some see the incident as a misunderstanding, equivalent to snatching a gun away from a child, but others say they would take the gun away from the child, "but I wouldn't shoot them dead." It makes This Troper wonder if Saren Arterius isn't the only Turian with A Dark Secret - the Turian Heirarchy had a "Unification War", maybe they have a Blue Sun Corporation?
 * Mass Effect: Evolution proves the initial poster right. The turians weren't pissed off about the relay, they were freaked out about an entirely new species showing up on Shanxi - which has Prothean ruins. The entire First Contact War was over those ruins, not the relay. Three more issues left in the series, but whatever happens forces the turians to make huge reparations to humanity, and makes the Illusive Man so paranoid about aliens and the Alliance that he spends the next few decades building an NGO Superpower to protect humanity from collaborators.
 * Whoever said humans in the ME universe are characterized by a "shoot first, ask questions later" mentality? For that matter, whoever said a turian couldn't have a "shoot first, ask questions later" mentality?
 * There's at least one turian who does have a "shoot first, a lot" policy: Saren.
 * Two turians. Remember what a loose cannon Garrus is when you first meet him?
 * I think this is a sign of just how unconsciously the concept of the Planet Of Hats has been ingrained into us. Like here, there's this idea that if the turians don't act explicitly like the stereotype in the Codex, something is apparently wrong. Nothing is wrong with a turian field commander being of a "shoot first ask questions later" mentality, any more than it's wrong for any particular human officer to act that way. That's a subtle point that Mass Effect is getting across. There is no Planet Of Hats here; just vague racial tendencies that are as often subverted as they are played straight.
 * Note that this is FIRST CONTACT meaning that communication by Universal Translators would have been impossible. The turians may very well have been trying to communicate with the humans but, unable to, may have attempted what was perceived as hostile actions (an alien shouting stuff at you and standing in the way of you doing something you think to be harmless... yeah, you might think that aggressive). Subsequently, the humans may have then responded with defensive measures of their own until all the miscommmunication builds up and someone fires a weapon that triggers a war. As what happens in a lot of wars and history, the facts of what happened may have simply been lost in the face of the bigger picture and of the subsequent political fallout especially considering our own limited knowledge of what happened. Both sides may have been right - they're just too invested in what happened (and too proud) to back down and try to settle things.
 * Again, Mass Effect: Evolution proves that something's rotten in Denmark. The turians figure out translators to understand humans during the conflict. They just refused to leave Shangxi without an as-of-yet-unknown Prothean artifact.

The Consort's Trinket

 * Where the hell did the Consort get the trinket? Seriously! A key that unlocks an ancient Prothean machine that triggers ancestral memory? Where did she get it?
 * She herself says it's a mystery. No further development is offered, though keep in mind, the Consort is implied to have unique mind powers. It's possible she acquired them from Prothean technology.

Doing missions after stealing the Normandy

 * Why is it that after you steal the Normandy you can't access the Citadel again, but you can still take on missions from Admiral Hackett, and land on places like Noveria (which would sell you down the river in a heart beat because of the trouble you caused there)?
 * Hackett's probably giving you the missions on the hush-hush. And you could equally argue Noveria would prefer the Council leave them alone, no matter the circumstances.
 * Because Hackett != the Council. He's Systems Alliance, and therefore doesn't operate within the Council's chain of command, and thus can give you missions without their approval or authority. And Noveria wouldn't be stupid enough to cheese off a Spectre, especially after you cleaned up their geth and rachni infestations.
 * It's worth noting that technically, the Normandy is also still Systems Alliance even if it was pulled out of the formal chain of command thanks to its commander's Spectre status, and it was also impounded under human authority (with the Council's tacit acceptance). Then again, Udina's a bit of a git, and there's no reason to think that Hackett has any better an opinion of him than Anderson does. Combine that with the usefulness of plausible deniability and the fact that Shepherd is still doing Alliance work, and Hackett could easily just shrug and keep passing along his little side jobs on the sly.
 * Noveria is willing to continue doing business with Saren after he is declared a traitor and is being hunted by the Citadel for acts of war. By comparison, Shepard simply stole a ship. If Noveria is willing to work with Saren in spite of treason, they're not going to bat an eye at letting Shepard dock.
 * The Council was keeping the name of the Spectre that had gone rogue a secret. No one on Noveria would have known Saren was a traitor.
 * Kalisa al-Jilani outright says that you're hunting a rogue Spectre named Saren, and the Council made a massive announcement with dozens of dignitaries present in the Council Chamber, on top of an equally public hearing about the same thing just before. If they're trying to keep Saren's treason a secret, they're doing a really bad job of it.