Mass Effect 2/WMG

Spoilers here for the second game. The first is here, and the third is here. Read at your own discretion.

The Collectors did something to them

 * Just before you get to Horizon you see the survivor of Virmire in the first game chatting it up with a local on the colony. Then the Collector ship touches down and a seeker swarm proceeds to paralyze both Ashley/Kaidan and the local. You do later see the Horizon colonist in the Collector Base, being broken down for genetic material to create the Human Reaper, yet after you defeat the Praetorian at the end of the Horizon mission, Ashley/Kaidan suddenly shows up perfectly fine. How is this possible? Ash/Kaidan was frozen not far from the colonist you see at the Collector Base, and it doesn't seem likely the seeker swarm paralyzation could have 'worn off' as by the time Shepard reaches the colony, there are still frozen colonists. What if the Collectors did something to Ash and Kaidan? Neither one seems to comment on being frozen, and Shepard has no idea they were hit, even though the player does. It's possible that due to the Collectors', and thus the Reapers' interest in humanity, they always intended to let Ashley/Kaidan, a hero of the Citadel, and a high-ranked officer of the Systems Alliance go, but brainwashed into some sort of sleeper agent. This would probably be to facilitate the taking of Earth, either in the creation of the Human Reaper, or simply when the Reapers came to clean house. Or more possibly, the Collectors turned Ashley/Kaidan into one of their agents as a tactic for dealing with Commander Shepard, due to their relation to Shepard as former teammates and fellow Alliance soldiers, and possibly as a former lover. Brainwashing could easily be accomplished through some form of indoctrination as well, and it's likely that neither Ash or Kaidan realize they've been indoctrinated in any way. Possible conflict in Mass Effect 3, pitting Shepard against the survivor of Virmire, now on the side of the Reapers?
 * Maybe the seeker bugs need to be near a Collector ship for the paralysis to work, for some technical reason. After the ship left Horizon, the effects wore off and that's how Ash/Kaidan was able to shake it off and show up at the end (that would also be why he/she wasn't able to help with the actual fight - he/she, and the rest of the colonists, was frozen until the ship actually took off). That would also explain how Mordin's seeker bug wasn't able to paralyze him - considering that the bug is almost strong enough to break the tank's glass and can "sting" through armor, it should be able to sting Mordin despite the tank arrangement, unless whatever causes the stasis is no longer functional. As far as Lilith goes, she did (finally) run away. Depending on where the Collectors started collecting, it would be possible for her to be harvested, but not Ash/Kaidan. Since Shepard saw the frozen colonists and didn't see anyone moving except the hidden mechanic, s/he probably did know or at least assumed that A/K was hit by the swarms, and just didn't get the chance to ask about it before the reunion went downhill. It would have been nice to be able to ask Mordin about that, though. He might know more about how the paralysis works.
 * The main problem with the theory is that Ashley/Kaiden didn't get paralyzed in the same area the colonist they were chatting with was. There was a bunch of chaotic movement. As to how they got loose, it's likely the Collectors intentionally released the paralysis so that Cerberus couldn't study the condition so that they could develop a much more effective countermeasure then merely baffling the swarms, which I wouldn't put past those Genre Savvy bastards.
 * This is kind of likely, considering how they handled the 'repercussions of not being loyal to love interest in ME 3'. They really are brainwashed, but come ME 3, their fate depends on how you handle your love life. If you stayed loyal, then they will shake off the brainwashing and run back to your side. If they weren't your love interest at all, they shake off the brainwashing due to The Power of Friendship, but unable to join back your team (at least they lived). If you cheated, they won't be able to shake off the brainwashing and you have to kill them.
 * I don't think it would be fair to lock them out of your team just because you didn't bang them in the first game. Maybe you'd need a Paragon or Renegade dialogue option instead to get them to come back. To be honest, though, I truly hope that nothing comes of it and that it's just that they got lucky in not being in the area from which the Collectors had been taking people when Shepard showed up. After all, I don't think the Collectors know or care what Ashley/Kaidan looks like or who they really are beyond that fact that they had a connection to Shepard, and therefore the fact that they were on that colony was a way to draw Shepard in. The Collectors/Reapers only took note of the name, not the person.

Ambassador Udina is a high ranking member of Cerberus, possibly even its leader.

 * When Admiral Kahoku's marine recon unit was lost, due to running across Cerberus activity, the system was placed under lock-down, preventing further investigation (until Commander Shepard was brought in). This benefited Cerberus. However, it was not a lock-down ordered and enacted by Alliance Fleet, as Kahoku was petitioning the Council, not his own commanders. This strongly implies it was a lock-down enacted by the Citadel Council. Given the spectacular unlikelihood of the Citadel Council itself seeking to advance Cerberus' activities, this leaves the "someone petitioned the Council for the lock-down" theory. And the only human other than Shepard who can even get the Council to listen to them promptly? Ambassador Udina. Who espouses beliefs akin to those of Cerberus in the Renegade ending.
 * Another data point is that Cerberus rapidly finds out that Kahoku has gotten past their bureaucratic roadblock, by asking Commander Shepard to do his investigating for him. This triggers their decision to abduct and kill him. But Shepard is a Spectre at this point, and everything they do is classified. The only people Shepard is reporting their activities to throughout the game are the Citadel Council... and Ambassador Udina. So, who told Cerberus that Kahoku was onto them? (While the Shadow Broker is a possibility, as Kahoku's investigation involved asking for help from the Shadow Broker, the Shadow Broker's agent will point out to you in conversation that it would have been extremely stupid for them to tip off Cerberus and get Kahoku killed before Kahoku could pay their fee.)
 * In the second novel, a character later revealed to be a Cerberus agent mentions off-hand that he supports Udina's bid for the Council seat. Suspicious, no?
 * Udina is obviously not the Illusive Man, but in one of the emails that Shepard gets on the new Normandy it says that Udina gave the sender a way to contact him. Another sign that says he's one of them.
 * The number of emails Shepard receives during the game suggests that it's the same one s/he had in ME1. Nothing really suspicious about it.
 * And if Udina is the human Councillor instead of Anderson, he doesn't even allow a reinstatement of your Spectre status, in addition to badmouthing you to the rest of the Council. How convenient for the Illusive Man, given that your gaping lack of other allies or resources is the only reason you're putting up with him at all.
 * This only happens if you killed the Council in ME1. If they survive and Udina is the human Councilor, your Spectre status can be reinstated.
 * True, but only because the council owes so much to Shepard that if he contacted them directly, and they learned Udina blocked Shepard's reinstatement, he could very well be kicked off the council. He doesn't want to do so, per say, but he has no choice.

If you choose the Renegade ending for ME2, Cerberus will actually be the Big Bad of Mass Effect 3.

 * It is heavily implied that, while Cerberus is dedicated to fighting the Reapers, they will turn against the other races of the galaxy once the Reapers have been defeated. This can manifest as either
 * They are not exactly happy with you in the Paragon ending, either. Some kind of adversarial role for them is extremely likely.
 * Considering in the Paragon ending, an adversarial role seems even more likely in that scenario.
 * Well, the Paragon ending is Lawful Stupid, as you'll need that tech to kill the Reapers I bet.
 * Yes, it's really smart to give powerful technology to terrorist organizations.
 * Honestly, letting people try and mess with Reaper tech is just stupid, it will probably indoctrinate them just like everything else related to reapers.
 * Dangerous, yes, but not stupid. Sacrificing a small number of people who can provide extremely useful data that could save the galaxy is not stupid. Besides, when the entire galaxy is at risk of extinction, some risk has to be taken. The biggest risk is Cerberus obtaining the ability to indoctrinate other races, essentially brainwashing the galaxy to serve man. Even with that, though, they would still be easier to stop than thousands of nigh-immortal dreadnoughts with the same ability.
 * No, the biggest risk is Cerberus getting indoctrinated and using all those resources and skills to help the Reapers.
 * History has taught us time and time again that just handing out dangerous military technology to people with no concern for ethics in their military or scientific operations is an extremely bad idea, even if it's to stop a more immediate threat.
 * Partially confirmed. Bioware has announced that Cerberus will move against Commander Shepard regardless of what happened to the base; though the Reapers will still be the main villains.

The Paragon ending of ME2 will not lead to a schism between Shepard and Cerberus.

 * The Illusive Man spent an insane amount of money on Shepard and the SR-2; EDI even goes as far as saying that it's a significant portion of the entire organisation's resources. It is thus natural that he has a bit of a temper tantrum when
 * Note that long before we can ask EDI just how expensive the Lazarus Cell is to maintain, the Illusive Man is adamant that the Lazarus Project can only work as an extreme, but calculated, risk. Miranda wanted to artificially control Shepard, for example, and the Illusive Man over-rode her because he sees Shepard as a necessary wild-card; controlling him makes the entire thing pointless. The entire thing is based less on the idea that he can convert Shepard to his way of thinking (his "good luck" speech before the Normandy hits the Omega-4 Relay comes to mind here) and more on the idea that Shepard is the man most likely to make things happen that will result in a favourable outcome to the problems at hand, even if that doesn't involve Cerberus ensuring humanity's dominance over the galaxy at large.
 * The conclusion here is that as much as the Illusive Man may hate Paragon Shepard's idealism and unwillingness to put humanity completely above the rest of the galaxy, he's still going to see Shepard as an indispensable asset; as much as the Illusive Man can do, he can rally others to fight for a common good about as well as a krogan can breed. He needs Shepard much more than Shepard needs him, which is why he had Shepard brought back from the dead to begin with. Cerberus continuing a relationship with Shepard, even if it means cutting back on their more morally questionable methods, will make Shepard's job a lot easier and is, thus, in the interest of Cerberus' goals for human advancement and preservation. He's extremely adamant that Cerberus' one goal is to safeguard and advance humanity, and despite all the questionable things Cerberus has done, there is a line he won't cross (witness ), and the Chronic Backstabbing Disorder both we and Shepard expect from the Illusive Man and Cerberus as a whole never actually manifests. Even Mordin says that Cerberus openly recruiting aliens and using AIs means that the situation is extremely dire; reviving a Paragon Shepard and letting him have free-reign on how to run his mission when the Illusive Man must know he'll never do something that benefits humanity if it means harming others as a trade-off is something you can add to that list. Losing is like a punch to the gut for him, partly because it was so close to happening that he could practically taste it, but he'll get over it; all it really means is that supporting Shepard won't get him what he wants, but will get him much more than he would have otherwise.
 * I'm inclined to agree. Rebelling against Cerberus seems more likely to play out as a power play for command of the organisation than an out and out cutting of ties.
 * Which line won't he cross? In the novels he sees nothing wrong with injecting untested experimental chemicals into an autistic child, blowing up ships above colonies to create biotics or kidnapping someone who pissed him off and implanting them with Reaper tech. In the games he has no problem having entire squads of marines be ripped apart by Thresher Maws and then experimenting on the survivors. According to Cerberus Daily News, Cerberus was running a camp where they kidnapped people, injected them with potentially brain-damaging drugs and made them perform biotic actions until at least one of them died of a brain hemorrhage. There is no line he won't cross to get what he wants. It's more likely that the only reason he disapproved of was because they didn't ask him first.
 * Presumably also because they were Not much of a future if you kill the best candidates for minimal benefit.
 * Points taken, but it doesn't invalidate the idea that the Illusive Man would consider Shepard worth all the trouble. If morality is completely meaningless to him, he is, instead, Genre Savvy enough to realise Shepard is the hero of the Space Opera they're all a part of; just listen to the conversation he has with Miranda in the opening about how much of a Canon Sue Shepard is no matter what choices the player made in the first game.
 * Basically, Shepard is, to quote one version of the first game, "...the closest thing humanity has to a hero...". TIM knows that Shepard is valuable, if not as a person, than as a symbol. And to quote Wrex, TIM feels that Shepard will bring humanity "...to glory whether or not you like it." Regardless of how Shepard acts, TIM knows that Shepard will do great things and TIM can piggy back on that success, whether overtly or covertly.
 * Also, a standard run through the game results in him making out like a bandit even without the Collector Base. The Normandy SR-2 has more surveillance gear than armor - and even if you don't actually build every single one of the upgrades you gather, you still have the plans! The Lazarus Project cost four billion credits, and the Normandy was another hit to the pocketbook, but it in effect he got a cubic buttload of revolutionary weapons and ship technology for his efforts - a lot of which was proprietary alien technology. By the end of ME 2 Shepard's made exponentially more than the project cost - the Collector Base would just be the cocaine-laced icing on a cake he's already enjoying.
 * : According to Bioware Cerberus is going to be out to kill Shepard.

Cerberus has a Freudian Excuse.

 * Finished a back-to-back play-through of both games and thought; turians tend to be short-sighted jerks when it comes to warfare. Salarians are often Morally Ambiguous Doctorates. The Council has exterminated one species, sterilised another, and reduced a third to refugees. The Alliance got fast-tracked past centuries of red tape for some reason - and Udina is a card-carrying Obstructive Bureaucrat, not a savvy statesman who could sucker it out of them. What If...
 * During the First Contact War on Shanxi, resistance fighters managed to get a fair-sized craft operational and attempted to evacuate a number of non-combatants to Earth. Officially, they were never seen again. Unofficially, they were captured by the turian peacekeeping forces - but were not recognised as human.
 * What would the peacekeepers think they were, then?
 * Husks?
 * Salarian doctors noticed that a number of the larger ones were "bloated with parasitic infections", "removed" and vivisected the "parasites", then were forced to "euthanize" the afflicted when they became inconsolably violent following the procedures. Many of the smaller ones starved to death, being unable to digest turian rations (why should the doctors who treat the turian peacekeepers go hungry to feed bizarre mutants when they had interstellar criminals to suppress?).
 * The starvation part is just silly, salarians are smart enough to recognize the Dextro-Amino acid barrier, which is the minority.
 * I doubt they'd fail to realize that the "infections" were pregancies, either.
 * Then a Child Prodigy among them got a hold of an omni-tool and hacked the airlocks. Aliens go whoosh and young Tim Howser becomes the proud owner of the Unrelenting Justice; a state-of-the-art turian dreadnought once commanded by General Kihar Arterius. He takes the ship back to Earth with his few surviving friends... and gets the run-around from the Systems Alliance. A little more hacking and he discovers that the Alliance has received loads of political credit and colonisation rights in exchange for avoiding a war crimes trial - and surrendering the remaining refugees.
 * There's an accident involving the Charon Relay and a ship-sized mass. Tim Howser, the refugees, and the Unrelenting Justice are gone and gladly forgotten. But some say that somewhere out there is Humanity's last, best chance for victory against Scary Dogmatic Aliens and their human collaborators: The Illusive Man, his few remaining allies, and their renegade ship - the CERBERUS!
 * Very nice, but all Jossed with the release of the comic series Evolution.

A Renegade Shepard with Miranda as the love interest will kill the Illusive Man at the end of ME3.

 * It would work as a power play to essentially have rule over humanity. Miranda would take control of Cerberus while Shepard would be in a position to usurp authority of the Council or Alliance.

Conversely, under Paragon Shepard, the Lazarus Cell will break off from Cerberus and become its own group.

 * If you bring Miranda with you to the final battle and choose to, she resigns from Cerberus. It stands to reason that Jacob and the rest of the group (if they survived) would also pledge their loyalty to Shepard instead of TIM.

Cerberus' main front is Sirta Foundation.

 * If you poke through crates while searching for Admiral Kahoku at the three Cerberus bases, you'll find a boatload of Sirta Foundation stuff - bio-amps, omni-tools, and the ever-so-fashionable (and overall useless) Phoenix-type armours. Why do they have such a large stockpile of this stuff? The answer to that question is that Cerberus is doing tons of medical and biotech experiments - an area in which Sirta Foundation excels at. They were the ones, after all, that created medi-gel - technically illegal, but everyone gives it the blind eye because it works. Sounds like what an "ends justify the means" company would do. Sirta Foundation is based on Earth, and is one of the mega-corps of the Mass Effect universe. Corollary: I wouldn't doubt that they had snapped up a piece of Conatix when that company went under. Sirta Foundation suffered a huge setback during ME. Now, the news article that mentions this is meant to refer to the "Besieged Base" Paragon mission in which you must kill biotic terrorists while saving five scientist hostages. Whether you save them or not, however, the news report still insists that Sirta was ruined by this attack (to the point of bankruptcy), indicating that there must have been something else that tossed their organisation to the crapper. Well, what if those four Cerberus facilities you shot up were also research facilities for Sirta?
 * The Sirta Foundation shopkeeper in ME 2 does express confusion why a human corporation would hire an asari for customer service. Almost like they had a reputation for being pro-human. And she does mention that Sirta Foundation isn't interested in profits. Almost like they have an even larger and wealthier organization backing them. Hmmm...
 * The "not interested in profit" seemed like corporate spin. I'm sure real-world drug companies make similar claims of only being in it for the good of mankind. The asari's confusion at being there was probably a reference to asari exoticism - a "sex sells" situation, that she just didn't grasp.
 * Believe it or not, ME 3 makes this seem much less likely. They're still operating, still selling supplies for the war effort.

Whether or not Cerberus is good or bad depends on Shepard's actions.

 * There is a lot of evidence supporting both views of the organisation, and how it will be remembered is ultimately up to Commander Shepard her/himself. If s/he is a Paragon, s/he will break off of Cerberus with a large number of personnel. The Illusive Man will become more extreme out of both anger and sheer necessity, and the only folks left in the organisation will be those most fanatically devoted to an anti-alien agenda. However, if Shepard is a Renegade and sides with Cerberus, they will be remembered as the people who took down the Reapers, and who have reformed since their early days of terrorist activity. This fits in with the general pattern in the ME universe that Shepard writes history. Shepard determines whether or not the rachni survive, and whether the Council lives, dies, or is replaced entirely by humans (among many, many other important decisions). It makes sense that s/he will ultimately decide whether or not Cerberus is remembered as an evil organisation, or a heroic group unbound by red tape.
 * Miranda, Jacob, and other Cerberus lackeys are keen to espouse how great Cerberus is, and that it does good work. At the moment, the only good things we've seen them do is build the SR-2 (which, in itself, is not a "good" thing) and resurrect Shepard (along with all the ethical baggage that comes along with it, which is sadly never addressed in-game). On the other hand, Bio Ware goes out of its way to show Cerberus' villainy is one step removed from that of the Reapers. They're assholes, period.
 * Bio Ware has shown a very selective and one-sided portrayal of Cerberus' "villainy". According to the Illusive Man the unethical Cerberus experiments Shepard has seen were rogue elements. He claims he didn't know about them at the time and he put a stop to them when he found out (this is at least partially confirmed in Jack's loyalty mission, where the recordings clearly say the Illusive Man didn't know what they were up to). True, this could be an elaborate deception on TIM's part, but it could also be the complete and unvarnished truth. We don't know for sure. So it's not fair to say they're "assholes, period".
 * The recordings never say what the scientists were keeping from the Illusive Man. Not to mention your argument is predicated on the idea that the Illusive Man wouldn't lie to you -- and we have proof that he has.
 * Yeah, and your argument is predicated on the idea that TIM would never tell you the truth. Read what I said again. It could be an elaborate deception on TIM's part, but it could also be the unvarnished truth. Either way, we (that is, you) don't know enough to say they're "assholes, period".
 * Not to mention that a lot of real life criminal and terrorist organizations do good things to maintain face. Villainy doesn't preclude acts of kindness any more than doing so morally balances out that villainy. You can save the world all you want but you're still kidnapping kids and experimenting on them.
 * I get the idea that Cerberus is set up to allow a certain level of Plausible Deniability. So a bunch of scientists get a lot of funding and are told to make the most powerful human biotic, with vague threats about failure. Then they turn around and let the scientists unlimited freedom with the funds they have. If they fail, then the Illusive Man will put on a big show and will have the evil scientists fired (out of an airlock), and will say how this was a rogue group. But if it succeeds, then Cerberus claims all the credit and says that they're doing to horrible things that keeps humanity alive.
 * I call bull. TIM had to know. When you unlock EDI, she specifically tells you that The Illusive Man likes to maintain personal oversight of all cerberus projects and that no one cell is aware of what the other does. Miranda is telling the truth when she says she didn't know what was done to Jack. There is no way that with the amount of resources involved to create the super biotic that is Jack, that TIM didn't know about it. All the evidence that is left is set to not implicate the main organisation but condemns the rogue elements. No more than a dozen projects at a time. Any more than that, and it stretches his multitasking ability.
 * Nope. They're evil no matter what you say or do.

Cerberus is completely on the level.

 * The opening scene to ME2 has Miranda and TIM conversing about recruiting Shepard. Basically they say that they need Shepard because the Council will trust him, but won't trust Cerberus. What can we draw from this? Cerberus wants to stop the Reapers and work with the Council to some extent. TIM really has no reason to hide information from Miranda, and no one else (save for a random messenger who gives TIM a data file) is present. As for knowing about the Reapers? TIM provides the flimsy excuse of "the information is in the patterns," but in reality he already knew about He simply wanted to play that hand close to the chest, so to speak, and keep that information from Shepard lest s/he run off and tell the Council about it.
 * in no way connects them to the Collectors. It's proof of their existence, but only the Council an idiot would doubt it after the Battle of the Citadel.
 * And TIM would only work with the Council and stop the Reapers because humanity is at stake. He honestly wouldn't care if it were happening to any other species and he needs Shepard/the Council because they have pull he does not.

Cerberus is behind Haestrom's sun's abnormal state.

 * The Geth are just a Red Herring. Consider the star that TIM has in his office. It changes color at the end, but it's not simply a case of Empathic Environment to reflect your Paragon/Renegade choice. It's because it's advancing into the next phase of its evolution.

Cerberus' influence stopped the Alliance from reaction to the Collector Abductions

 * During the abductions of human colonies by Collectors, the Alliance did not exactly much. Neither did the Council, of course, but that is a different story. That despite the fact that entire colonies disappearing cannot simply be handwaved away like naming the Sovereign attack on the Citadel a geth attack. Additionally, the Alliance knows at least something about the Reapers, as seen by Kasumi's greybox memories and their non-contestion of the turians breaking the Treaty of Farixn (Cerberus Daily News).
 * Now we know that Cerberus has its claw deep in the Alliance, given TIM quite a potential pull in it. So, the reason that the Alliance does not do anything coherent about the Collector threat is that TIM has his contacts in the Alliance apparatus prevent any such action.
 * That way Shepard is forced to cooperate with Cerberus, as the Alliance just won't do anything about the problem while Cerberus does. TIM gets a galactic hero under his thumb (his attempts to alienate Shepard from his former squadmates is part of that effort, too), and said hero working with Cerberus is of course also prime PR material. The Normandy-SR 2 is openly flagged as Cerberus, and as per the prologue cutscene TIM seeks some cooperation with the Council. So, using Shepard as face might be a attempted first step into respectability for Cerberus, and as such TIM made sure Shepard had no alternative than cooperating with him.

SCP Foundation.
 * It's an extra-governmental agency whose main goal is the development of humanity, they accept the existence of Reapers (an anomalous thing if ever there was one), they have no problem with questionable experiments...

The Illusive Man will be the Man Behind the Man in Mass Effect 2.

 * He was helping the Collectors abduct humans in exchange for data from their experiments that he could use to make super-soldiers. When he sees that the Collectors have Reaper technology, he sends Shepard on a suicide mission to kill the Collector Hive Mind so he can use the Reaper technology to make humanity stronger. Shepard will learn this at the end of the first disc and will defect from Cerberus, along with all of his allies that are loyal to him.
 * It does seem likely that you end up making some move against TIM in the endgame - previews have said that not earning your team's trust can cause them to betray you, and turning on you for betraying Cerberus and TIM is the only plausible motivation for Miranda (and possibly Jacob, although information so far has him painted as far less of a company man).
 * You don't fight Cerberus at any point in ME2. Whether you fight Cerberus in ME3 remains to be seen, of course.

The Illusive Man is Armistan Banes.

 * It's stated in the first game that Banes faked his own death, and Cerberus used to be part of the System Alliance or at least had relations with it until they went rogue. Banes clearly makes shady deals for weapons, is known to Alliance brass, including Anderson. And we've never learned TIM's name. It's obvious that they're the same person.
 * Kahoku also tells you that they found Banes' body on board a drifting freighter. So it's unlikely.
 * Nope. His name's Jack Harper.

The Illusive Man is CSM.

 * Both have remarkable similarities. Most obviously, they both are hardcore smokers. They also are mysterious omniscient men who are (possibly for the Illusive Man) collaborating with an alien species bent on galaxy wide domination and indoctrination. In addition, both cover up the truth from the public and manipulate a well intentioned agent (Mulder and Shepard) to do their dirty work.

The Illusive Man is connected to the Reapers.

 * The Reapers have an obvious interest in humanity by the end of the second game. Here's how I see it going down: Cerberus broke away from the Alliance military some time around the events of The First Contact War during which humanity, being the newcomer to the galactic stage managed to stand up to the strongest military in the galaxy. This would have piqued Sovereign's interest in keeping an eye on humans as a potential species for . It sets in motion Cerberus' break from the Alliance with TIM at the helm. Cerberus, under the guise of a hardline pro-humanity agenda, begins conducting all manner of experiments on human potential and TIM, being the only individual privy to the entirety of Cerberus' operations, forwards the results of the organisation's research on to Sovereign itself. Then Shepard comes along: a celebrity among humans for being able to survive and/or succeed against impossible odds and later becoming the first human Spectre, furthering Sovereign's belief that humans would be the best candidates for . Before the attack on the Citadel, it sends the information it has gathered to the Collectors to begin harvesting humans for . As an extension of this: TIM is a highly advanced or prototype Husk. Though his eyes could be the result of modification, they also bear a resemblance to husks in colour if not luminosity. He is always seen smoking with a glass of alcohol by his side, lung and liver damage not being a concern if he is, in fact, synthetic.
 * It's mentioned in Retribution that things like cancer are cured, and so there's no real risk to cigarettes or alcohol. If TIM is working with the Reapers, he isn't aware of it. Retribution, again, has several chapters from TIM's point of view, and it makes it very clear that he wants to defeat the Reapers. Given the nature of indoctrination, though, it's possible - albeit unlikely - that he may be doing their bidding without realizing it.
 * Considering
 * Further weight to this theory: The effect of Reaper indoctrination on Saren's eyes looks remarkably similar to the Illusive Man.
 * As of ME 3, TIM is definitely connected to the Reapers, but in some very interesting ways.

The Illusive Man specifically tried to keep Shepard away from Liara in Mass Effect 2.

 * During one of the early meetings with the Illusive Man, where you can ask about your former party members, the Illusive Man states that Liara "is working for the Shadow Broker, she can't be trusted." Yet when you do eventually run into her, she's actually working against the Shadow Broker, and has done so since before Shepard's resurrection. How could the Illusive Man be so wrong about her affiliations? That's just it: he wasn't. As the Illusive Man proudly states, information is his weapon, and his information is never wrong. Except, of course, when he's purposefully lying to Shepard. The question of why he would make such an effort to keep them apart is currently up for interpretation, and will likely be answered in the Mass Effect comics; this troper's guess is that Liara knows some deadly secret about Cerberus or the Illusive Man, and it is only her private crusade against the Shadow Broker that kept her distracted enough that she hasn't yet told us what it is.
 * Well the comics do show what Liara's relationship with Cerberus was. At any rate, one alternative is that he's trying to keep Shepard distant from his friends so that 1) Shep's easier to control and 2) information not in the Cerberus point of view can be limited.
 * He seems to be employing a kind of Jedi Truth. IIRC, TIM's exact words are "my sources say [Liara] is working for the Shadow Broker". Which may technically be true. TIM's sources could me mistaken and TIM could be smart enough to know it. Regardless, it's unlikely he was trying to keep Shepard away from Liara. Recall that at that point in the game the Shadow Broker is not yet established as an antagonist. They were vaguely sinister but not yet villainous. More likely TIM was testing Shepard's priorities. If he stays away from Liara, TIM knows Shepard is unwilling to compromise his/her principles by working with morally ambiguous characters, which does not bode well for Shepard's continued willingness to work with Cerberus. If Shepard goes to see Liara anyway despite believing she is an agent of the Shadow Broker, TIM knows Shepard is willing to use morally ambiguous means to achieve his ends, which means Shepard is less likely to betray Cerberus later.
 * Possibly, TIM is trying to keep Shepard from distracting Liara. TIM knows the Shadow Broker is a threat to him, and wants the Broker taken out. Liara is doing TIM's work in going after the Broker. He was worried, though, that if Shepard showed up and asked Liara to re-join the crew, Liara might agree, thus taking her away from her hunt for the Broker - possibly permanently, if the mission doesn't go well. So TIM was hoping to keep Shepard away from Liara until Liara finished her work.
 * Precisely. Once TIM has the relevant data, he hands it right over, and it's off to The Lair Of The Shadow Broker!
 * Seeing how LOTSB ends, I'd say this plan backfired if it was the case. Not only did Liara get a better chance against the Shadow Broker with Shepard's help, but it also got Shepard an actually loyal ally at least as powerful as Cerberus.
 * Further evidence: the information that Cerberus gives you in their e-mail says: "we'd appreciate if you could hand over the data as a gesture of goodwill." It never says anything about helping Liara yourself. Perhaps Cerberus were hoping to get Liara killed for some reason? Also, TIM's notes at the end of the mission say that "The asari's relationship with Shepard should be watched closely." Something going on in the dark, perhaps?
 * My theory is that he's trying to keep Shepard away from former allies until he's sure they won't interfere with the mission. Remember: with Horizon, he leaked information of Shepard's connections with Cerberus to the Alliance, knowing already that Ashley/Kaidan was on Horizon. It could be his way of testing whether Ashley/Kaidan would follow Shepard even knowing about the Cerberus ties (didn't work). Wrex was too busy rebuilding his clan anyway, Garrus was an accidental reunion (as TIM was unaware of Archangel's identity), and Tali only became an option in his eyes after she took care of her unfinished business. Similarly, he didn't mention Liara until it turned out she was necessary to track down Samara and Thane. Not to mention that TIM and Miranda had met Liara before and knew she didn't agree with their methods, and only cooperated with them that one time on the off chance they could bring back Shepard, and the alternative was even worse.

The Illusive Man will become indoctrinated.

 * His Knight Templar demeanour and trust in his own superiority makes him a perfect successor for Saren, and it's not that big leap from ensuring humanity's superiority at whatever cost to turning the humanity into a Reaper with a bit of mind manipulation.
 * This would be the perfect excuse for Bioware to

The Illusive Man will attempt to kill your love interest.

 * This will happen regardless of the choice you made at the end of Mass Effect 2. If Shepard made the Paragon choice TIM will attempt to kill your love interest for revenge. If Shepard made the Renegade choice TIM will still attempt to kill the love interest because "I need you focused and s/he is a loose thread we can't afford". Obviously this will have a sadistic choice; save your love interest or stop The Illusive Man once and for all.
 * Nah, he's trying to kill you.

If you chose the Renegade ending for ME2,

 * Think about it - so far most Cerberus operations seem to end with the entire team involved dead, and very little actual pay-off (you being the biggest exception to this trend, and only by the skin of your teeth). Cerberus will be an enemy in ME3 no matter what - if you went Paragon, . If you went Renegade, it's because
 * Well... the only reason most operations we encounter are dead is because Cerberus isn't exactly concerned about lives on an individual level. They're willing to sacrifice a few to serve their ideals.

The Illusive Man's real name is Tim.
It doesn't make any sense for such secretive and paranoid man to make an acronym of his alias spell out his real name. But then again, it's Wild Mass Guessing. It doesn't have to make sense.
 * No, no! The Illusive Man's real name is Tim! Evidence: he's always smoking! (Okay, so maybe he's toned it down a bit...)
 * Comedy aside, Evolution reveals his name as Jack Harper.

The Illusive Man doesn't look anything like the image he shows.
"Illusive Man: No, Miranda. I am your father! *Imperial theme*"
 * Illusive means "based on or having the nature of an illusion." Given his paranoia, him allowing anyone to see what he looks like would arguably be out of character.
 * Two problems with this. First off, Miranda and TIM are in the same room at the start of ME2, and he looks the same as when he and Shepard speak to each other. Secondly, there's a new comic series coming out about the Illusive Man, set during the First Contact War: he looks younger, but still very similar (like a young Martin Sheen, in fact). Part of me wants this to be true, though, just to get this line in:


 * Actually, we get to see him in person in ME 3, and he looks like his hologram. With some alterations, at that point.

You will have to fight The Illusive Man in Mass Effect 3.
If you destroy the Collector base, he is very clearly pissed at you, and will try and take you down, believing that without the Collector tech, they won't be able to fight off the Reapers. If you decided not to, the Illusive Man will have everything he needs, and Shepard will have outlived her/his usefulness.
 * A recent magazine article stated that, among other things, Cerberus will be gunning after Shepard. Your reasoning seems the most likely; Mass Effect 3 will apparently begin with Shepard on trial after the events of Arrival, and it's more than likely that The Illusive Man will see him as too costly to use, regardless of whether you saved the Collector base, thus making him a Wild Card. Shepard did destroy a solar system, after all.

The Illusive Man is the Emperor of Mankind
Cerberus's goal and, therefore TIM's, is to make sure humanity prospers no matter the costs. He's not going on xenocidal crusades yet, because it's not necessary yet. Not much is known about him and he's a Manipulative Bastard.

Even after the Paragon ending, the Illusive Man does not consider Shepard a lost cause
He is going through an extended, post-game Villainous Breakdown, and committing the sunk costs fallacy. After spending billions of credits bringing you back to life, he is desperate to bring you over to Cerberus' side, even if he has to stoop to petty bribery... which is why DLC installed post-Paragon ending still comes from Cerberus. "Maybe if I send Shepherd a new set of armor, s/he will realize how profitable working with Cerberus can be."
 * As well as other assignments which have Shepard hopefully try to rectify projects. David is still alive at the end of Overlord regardless of ending. The Illusive Man can now do to him what he has done to Grayson in Retribution...and if Shepard rewrote the heretics...
 * Confirmed, actually. You can find a video log where he mentions he hasn't written Shepard off completely yet.

The Illusive Man is someone's father.
Because this is a space opera that loves to do shout outs. Odds are high on him being Shep's dad (complete with branching paths to explain how he hid the truth for each possible origin), but he could also be Jack's, right?
 * Not as far as find out.

The Illusive Man has the Mangekyo Sharingan.
Or some kind of regular sharingan-byakugan combination.

The Illusive man uses Electronic cigarettes.
Seriously, every time you see him, that cigarette never changes length.

The Illusive Man is so obviously a KI.
Of course, there are the eyes. Looking mechanical, electronical even. But, even more so, there are his habits. He is always drinking, smoking, doing organic things. Oh, look at me, how human I am, doing human things. Are we not all humans here? Come on, you are fooling nobody.

TIM knew that Archangel was Garrus.
The post-mission report says, "revelation of identity as Garrus Vakarian useful in keeping Shepard comfortable." It seems likely that TIM knew who Archangel really was, even when nobody else did. Just goes to show how much of a Magnificent Bastard he is.
 * Not only that, but TIM had arranged the situation Garrus found himself in. TIM might not have anticipated his (arguable) attempted suicide by merc, but the fact that his entire team was dead, leaving him free and clear to join up with Shepard? Way too convenient, even if he didn't know who Archangel was. Then, if you take the Paragon option through to the end for Garrus' loyalty mission, you find out that Sidonis had been threatened into betraying his team- and you never do find out who did that . . ..

TIM is Cylon Number 7

 * His eyes are clearly artificial. And as a machine, he can sort through tremendous amounts of information easily.

The Normandy SR-2 eezo core was once Sovereign's.

 * It's only mentioned in a Game Informer magazine preview, but there's a picture of it, and the core is a reddish metal sphere with a few red blinkies on it, a far, far cry from the SR-1's Tantalus core. According to the article, the writer specifically asked Bioware why it looks so different, and they wouldn't give him an answer, confirming that even if this theory is wrong, it's at least plot-relevant in some way. Really though, just look at the ship; the fact that it's highlighted red instead of blue can only be symbolic of two things; either the fact that Cerberus, not the Alliance, built it (red features prominently in Cerberus-themed material, like the Cerberus Systems network the website is presented in the form of and the in-game menus, which even have the logo in some places.) Or that Cerberus built it with Reaper technology. Since a red motif is also evocative of Sovereign, it's possible that the two ideas are not mutually exclusive, and much of what Cerberus does is based on Reaper tech.
 * The importance would seem to halt at it being I would still say the original guess has some merit, though, because another part of the game gives us another clue; not only does the core look nothing like the original,  Could be revisited in the third game.
 * Played the game. The core looks pretty similar to the first one, and doesn't really do anything spectacular.
 * You might want to play the first one again, because the SR-2's engineering deck and eezo core look absolutely nothing like the Tantalus drive system, which wasn't even self-contained, let alone stationary and spherical.
 * Very very loosely, they're similar. But it's like saying the kitchen is in front of the living room. Basically, the cargo bay leads to two corridors that join together again that lead to a small walkway to the core with an elevator between those two corridors. The general shape is there but the size differences and such mean that's about as far as the similarities go.
 * Has some merit once you go back and play the original game. When you speak with Sovereign on Virmire, he drops the quote "We are Legion." EDI was pretty quick to drop that same quote for
 * EDI flat-out states

The Normandy SR-2 will become a Reaper.

 * Cerberus installed in the new Normandy a computer called EDI. It appears to be a little bit more than just a VI as it snarks back at Joker. So either someone is controlling EDI remotely, whoever programmed it knew about Joker's personality, or it's an actual AI. If the last one is the case... ARE THEY OUT OF THEIR MINDS?!
 * It is an AI and it will turn into a Reaper and it'll be the final Big Bad in Mass Effect 3.
 * Okay, that's kind of awesome.
 * An AI that goes rogue does not immediately become a Reaper. At best they would join with them, but there's no indication that the Reapers would accept it.
 * And considering that it seems that there's a geth squad mate coming up, EDI might just as well become an envoy between organics and synthetics, if she's indeed an AI - though it must be remembered that VIs can be programmed with apparent personalities as well, up to making realistic simulations of historical figures.
 * It's still a valid theory for ME3.

Joker brought the scale-itch onto the Normandy.

 * Remember how EDI said that some of his extranet bookmarks are technically illegal in the Citadel space? He's clearly a colossal Covert Pervert with a list of weird fetishes as long as your arm. He saw some ad about tame varrens in Omega, and.. the rest is history you don't want to recall too well.
 * That porn clip we hear Joker playing? It's actually the scream female mercs use when they're Pulled by biotics. Joker is a sadist as well!
 * Could be biotic porn.

Joker is a spy for the Council.

 * The Council knows precisely what's going on, because Joker is telling them everything. Joker doesn't have very strong motivations to be loyal to Cerberus, and he has plentiful opportunity to keep in contact with the Council. He's also distrusting of EDI. And he That's him revealing his true allegiance to Shepard, and showing him what the Citadel Council has been working on all along. This is why the Council is so unconcerned about what Shepard is doing - because they are already keeping tabs on it, and know well enough that Shepard can handle it on his own, and they are concern that cooperating too closely with Shepard would blow Joker's cover within Cerberus.
 * Small problem with that: That thing on the datapad? That's

Kelly Chambers brought the scale itch onto the Normandy

 * Besides her character, when you talk to her about the new crewmember archangel, she says something along the lines of "holding him tight" and "comforting" him. When asked if she has an alien fetish, she comes with the anwser that she loves everyone equally, intimacy breeds compassion, and all affection is welcome. Its possible she takes that last bit of life wisdom a bit more literal than most of us.

Kelly Chambers is a spy for the Illusive Man.

 * She even says that she was picked by the Illusive Man himself to serve on the new Normandy. She would be a good choice for setting on the ship as a spy, as nobody would suspect a cute, flirty Bridge Bunny to be personally spying for the Illusive Man. She has access to Shepard's personal correspondence, and it is her job to keep tabs on all the squad members. Her flirtyness with Shepard is just a way to keep him or her off guard and defuse any suspicions. However, during the course of the game, she begins to develop genuine feelings for Shepard, and those feelings intensify if she is rescued. In Mass Effect 3, she will be torn between her loyalty to the Illusive Man and her love for Shepard. There will be a sidequest that, if completed successfully, will have Kelly sever her ties with the Illusive Man and possibly be a full love interest of Shepard's.
 * Her spy status is confirmed. But there's no conflict in her - she's ex-Cerberus, pure and simple.

The true purpose of the Lazarus Cell was a Plan on part of the Illusive Man to recruit Shepard into Cerberus.

 * Not only did Cerberus build a bigger and better Normandy and give Shepard a really, really nice captain's quarters, but the Illusive Man also hand picked the entire crew. You'll notice that all of them have very positive things to say about Cerberus and that Cerberus will "look out for its own" by doing things such as paying the transportation expenses to get a crew member's family off a colony before a Collector attack. Now, we all know that the Illusive Man is a Manipulative Bastard, so it stands to reason that he had Cerberus spare no expense to see to the needs of the Normandy crew so that they could unwittingly do their real job: convincing Shepard (and the player) that Cerberus isn't all that bad. With this in mind, Kelly Chambers' role as a potential love interest becomes suspect as well. In addition, why else would Miranda, the Illusive Man's most loyal operative, be assigned to the Normandy as Shepard's XO and spend nearly the entire time trying to convince him that Cerberus is just a Well Intentioned Extremist and that they only did what they had to.
 * I figured Kelly was TIM's spy on the Normandy, covertly gathering intel on the squadmembers and crew. Miranda is just too obvious, and as for being assigned as XO, she's TIM's right hand, and is the head of the Lazarus Cell (which includes Project Lazarus and the Normandy.). It makes sense he'd have her continue monitoring his investments once Shepard's up and running again.
 * And holy shit, Kelly was monitoring Shepard's mail. For all we know, she's been deleting all the emails from the Citadel and the Alliance, and sending snooty replies back to them in Shepard's name. Now I really like the theory - Kelly is a spy for TIM, and Joker is a spy for the Council.
 * Of course Kelly's priorities might change a bit when it's Shepard who while TIM makes snooty speeches about how Cerberus looks out for every human.
 * To be honest, it would be refreshing if a crew member didn't turn on Cerberus after
 * Because
 * Or:
 * On the other hand,
 * Remember what happened to them the last time they played around with some reaper tech? You can see why they do not like the idea of trying that again.

The Illusive Man deliberately picked less-extreme Cerberus members for the Normandy crew.

 * Notice how the crew consists entirely of either Alliance ex-pats like Jacob, former SR-1 crew like Joker and Chakwas, or hand-picked recruits like Miranda and Kelly? None of them act anything like the extremists we dealt with in ME1. Perhaps TIM knew that Shepard wouldn't trust the usual Cerberus goons, so he hand-picked crew members for the SR2 whose world views were closer to Shepard's, and whose loyalty to Cerberus might otherwise have been questionable. For all we know, even Miranda might be one of the more open-minded of the "real" Cerberus operatives (IIRC, she never has any qualms about Shepard hiring non-human crew members, and she even sides with you if you choose to ). This would have the side-effect of making Cerberus look less extreme than it really is, which would make Shepard more likely to work with them by taking advantage of the "no one is Always Chaotic Evil" theme that the rest of the game has been setting up. Best case scenario: It works both ways, as working with Shepard would make the crew more loyal to Cerberus by proxy. Worst case: everyone dies in the suicide mission, which is fine since, aside from Shepard and maybe Miranda, they were expendable to begin with (TIM says as much in an email if you ). Devious but brilliant. The only hitch in the plan would be the Paragon ending, where you survive and
 * Confirmed in a video log in ME 3.

Kelly Chambers is Obfuscating Stupidity.

 * Kelly's posting on the Normandy makes no sense whatsoever. You don't need a Yeoman - Shepard himself says it's a task better suited for a VI, and the Normandy has an Artifical Intelligence. Her sole value is that of the Sexy Secretary, or her degree in psychology. What use is that? Well, plenty, when you realise that the team Shepard is building is made up of criminals, psychopaths, guns-for-hire, and are mostly aliens working for a human-supremacist organisation. Kelly pretends to be a Valley Girl to put the nutjobs at ease and make herself appear non-threatening. In reality, she's constantly sending detailed psych reports back to the Illusive Man, letting him know how well the team is working together. This also works for the human Cerberus crew. Most of them are there because "Cerberus gets the job done!", or they really have nowhere else to go (See: Joker, Chakwas, Ken, even Miranda). The Illusive Man wants to know if any of them are slipping.
 * Well... having a psychologist on board is handy when most of the crew has issues that need taking care of. So there's that.
 * If so, she's not obfuscating very well. She outright says her real job is to talk to people to evaluate their psychological condition.

After the Lazarus Project, Shepard is now part Reaper.

 * This isn't as crazy as it sounds. Shepard now has weird red scars and (potentially) red glowing eyes of doom. Would qualify as an ultimate twist, and be a cool plot point later.
 * Maybe...previews of the ME2 prequel novel, Retribution, state that TIM is trying to implant Reaper technology into a human. Bit of a coincidence that he suddenly comes up with a way to bring people back from the dead afterwards?
 * Retribution has been confirmed to take part after the events of Mass Effect 2. The idea of having Reaper tech in Shepard, however, is still valid. Cerberus was performing experiments on Husks, and as we all know, the tech in them reanimates dead flesh. This tech may prove vital at the end of the trilogy - as it allows Shepard to sneak aboard Reaper-controlled stations and ships, or to resist indoctrination. I doubt Bioware had Shepard die and brought back as a cyborg simply to make players Restart At Level One.
 * The first pages of Mass Effect: Retribution confirm that the theory of Shepard being a Reaper is impossible. The Illusive Man made it so there's nothing in Shepard's body to be controlled, not by him, nor by anybody else but Shepard him/herself.

The Illusive Man is using Shepard to test Sovereign's mind control.

 * An expansion of the above theory, not only did the Lazarus Project implant Shepard with Reaper technology, the Illusive Man is using it as a test to see if a human can use the Reaper's indoctrination process to control other people: he sent Shepard to gather people who would normally never side with him to see if the technology will activate and force them to come with him when they normally wouldn't. Images show that Shepard gradually becomes more and more glowy throughout the game; the Reaper technology inside her/him is activating more and more as s/he has to keep control of his more volatile squadmates. Shepard is unaware of this until near the end; a Renegade Shepard will embrace the implants and use them to dominate his crew, while a Paragon Shepard will desperately search for a way to deactivate or remove the implants though there is another possibility. The Illusive Man is performing similar experiments on himself; this is evidenced by the implants in his eyes. The final level will be Shepard and crew going to the Cerberus base and fighting their way through to TIM, only to find that the experiment is complete and TIM has turned himself into a mind-controlling uber-cyborg, sort of like Saren. The final battle will be either a battle of wills between Shepard's mind control and TIM's, or the squad fighting him while Shepard uses his Reaper technology to shield them from TIM's abilities. In the end it will be revealed that TIM was indoctrinated by Sovereign before the first game started and was deluded into thinking he could use the technology to control the Council for humanity.
 * Shepard only becomes "more glowy" if s/he makes Renegade decisions, and you can eventually get rid of the scars altogether. Implanting Shepard with Reaper technology is just too dangerous, which is why he's using someone else - Paul Grayson. See Mass Effect: Retribution.
 * Jossed.

Miranda is the

 * Miranda assuming she's right and never questioning that, on the other hand, is perfectly in character. She's not the type to be self-doubting unless serious evidence gets brought up. And even then, well... see her loyalty mission.
 * Everything about that mission was too convenient. How do we know Shepard wasn't moved while unconscious to a facility that's effectively one big holo-room, Wilson and Jacob were kept in the dark about it being a simulation to make things more 'believable' and the shot Miranda fired never killed him, only knocked him out, but the stations holographics, combined with a stasis field made him appear otherwise. That way they can test both Shepard's loyalty and combat skills in an environment completely under their control.
 * You don't think Jacob or Wilson would have noticed that this wasn't the station they'd been working on for two years? Or are you gonna suggest they were tranquilized and moved as well? Not to mention the Fridge Logic of the fact that if you die in the prologue you just die, you don't have the simulation end or anything.
 * Jossed: At the end of Lair of the Shadow Broker, you gain access to the Shadow Broker's files in-game. One of them contains an offhand mention that Wilson was the Shadow Broker's agent inside Project Lazarus.
 * You don't think Jacob or Wilson would have noticed that this wasn't the station they'd been working on for two years? Or are you gonna suggest they were tranquilized and moved as well? Not to mention the Fridge Logic of the fact that if you die in the prologue you just die, you don't have the simulation end or anything.
 * Jossed: At the end of Lair of the Shadow Broker, you gain access to the Shadow Broker's files in-game. One of them contains an offhand mention that Wilson was the Shadow Broker's agent inside Project Lazarus.

Miranda, if Romanced, choose the Engine Room for a tryst as a Take That to Tali

 * Given how intelligent, and probably observant she is, Miranda likely knows that Tali has a thing for Shepard. Having sex in the Engine room will likely leave traces a Tech Specialist like Tali can pick up on. Bitch.

In Mass Effect 3, the Normandy SR-2 will get significantly upgraded to become the SR-3.
It's a logical progression: ME1 had the SR-1, ME2 had the SR-2, so ME3 will have the SR-3. However, rather than coming up with another Contrived Coincidence to get the Normandy destroyed again, BioWare will simply stick new tech on it until it's got upgrades coming out its exhaust ports. These upgrades won't completely take, requiring a Han Solo-like technician to make sure everything stays running smoothly. This will also add another Normandy-centric crew member, to continue another pattern of have having X crew members specifically for the Normandy in Mass Effect X - ME1 had just one such crew member (Joker), ME2 had two (Joker and EDI), so ME3 will have three (Joker, EDI, and Most Definitely Not Han Solo). More intra-ship snarking and rivalry will ensue.
 * Apparantly sort of confirmed and Jossed at the same time. The SR-2 IS upgraded, in ME 3, but so far only internal differences are mentioned. Exteriorwise the ship looks exactly the same, just repainted in Alliance colors. It's also still called the SR-2.

EDI was a late addition to the Normandy SR-2.
This troper was starting over to get the last two achievements and had a thought pop into my head during the early walkthrough of the Normandy just after the Freedom's Progress mission. There are a lot of empty command consoles in the front section of Deck 2, just behind Joker's cockpit. Yet only two of them seem to be occupied, and the Normandy's crew does seem a bit small for so many consoles. Perhaps EDI was added when TIM realized he couldn't find enough crew Shepard would find suitable (See the above WMG about Cerberus picking non-extremists), so an AI was put in as a compensation for this. This could possibly seen as a reason why it's in the Med Bay: the room containing EDI's core is actually just a medical storage room that was repurposed. 'They're running on a bare-bones crew so they don't need as many supplies, we can slap the AI core in right there!'

The Collectors are building a new Reaper.

 * The Enemies of ME2 movie confirms that Husks are, in a way, modular. It also confirms 20 Husks can be squashed together to form a Praetorian, a large flying machine that in no way resembles the Husks it was made from. What if that's a small-scale version of how Reapers are constructed? Squashing together of hundreds of billions of Husks made from various species, and the next stage of construction requires human Husks?
 * Expansion of prior idea. The new Reaper is a backup plan by Sovereign, in motion since whenever he indoctrinated the Collectors, so that should the unthinkable happen and he be destroyed (unlikely but non-zero chance), there will be another to continue his mission. Now that Sovereign is dead, the Collectors got the "go-ahead" on the less covert, more desperate resource collection parts.

The Collectors only have

 * They send one ship to attack the Normandy, then to attack Horizon, and when you finally go through the Omega-4 Relay you find  Either not all of the Collectors are working for the Reapers  or else they only have the
 * Seeing as the Collectors only attacked colonies outside of Alliance space, it makes sense the Collectors would want a low profile. Less ships means less suspicions.
 * At least in my playthrough,
 * Keep in mind that the "mere" hydromagnetic cannon was reverse engineered from Sovereign's weaponry. During the battle for the Citadel, Sovereign was one-shotting cruisers left and right, while it took a whole fleet to take him down. The Thanix cannons may not be as powerful as the Reaper Originals, but they are a massive improvement over any other weapons technology any contemporary race has.
 * The frigate doesn't even need the Thanix cannon to take down the Collector ship. Joker can still kill it if you didn't upgrade, it just
 * The Collectors' plan was basically a stealth operation. If they were going after Earth, (which is never confirmed, only speculated), they would probably build more ships and/or get direct Reaper support.
 * It's possibly it would have gone like this... build one Reaper and so you now have two. These two build up more forces allowing them to get more people-paste to build more. Repeat slow expansion while advancing towards Earth in addition to Reaper Fleet clearing the way from the other direction. Eventually, you'd have a bunch of Reapers coming from all over the place.
 * Alternatively, they are expecting the millions of casualties that would occur during an invasion and are only planning on taking who is left.
 * It's possibly it would have gone like this... build one Reaper and so you now have two. These two build up more forces allowing them to get more people-paste to build more. Repeat slow expansion while advancing towards Earth in addition to Reaper Fleet clearing the way from the other direction. Eventually, you'd have a bunch of Reapers coming from all over the place.
 * Alternatively, they are expecting the millions of casualties that would occur during an invasion and are only planning on taking who is left.

The Collectors' insectoid appearance

 * The Prothean statues on Ilos don't look very insectoid, yet their picture is used in the new Codex-article about the Protheans. According to Mordin only a fraction of the original Prothean DNA survives in the Collectors, implying that the rest was engineered or repurposed from other species. It would make sense that the Reapers would recycle genetic data they found useful in the past in generating yet another race of fanatic servants. The Collector-General is modified even further, or possibly doesn't have any Prothean DNA, at all.
 * The keepers are pretty buglike too; the Reapers may well have some kind of 'standard template' they use for all their slaves, with various modifications derived from useful features of the species they're adapting.

The Collectors are a mishmash of every species conquered by the Reapers that wasn't used to make a new Reaper.
Similar to the above. EDI mentions that the Collectors share DNA with Protheans, but have been modified to a great deal. Protheans are the only ones we know of, but there others before the Protheans, and others before those. It's a process that has gone on for at least 37 million years, with a ~50,000 year gap. 50,000 goes into 37 million a lot of times. Each time, the dominant race is either melted down and turned into a Reaper, or their DNA is added to the great melting pot that is the Collectors.

Collector tech is behind Haestrom's sun's abnormal state.
During Tali's recruitment mission, she mentions that Haestrom's sun is aging prematurely as a result of dark energy. However, a second playthrough of ME2 reveals a blink-and-you'll-miss-it line from Veetor on Freedom's Progress: "I recorded [the Collectors] with my omni-tool. Lots of readings. Electro-magnetic. Dark energy." These are basically the only references to dark energy in the series. Therefore, due to The Law of Conservation of Detail, the Collectors must have something to do with the sun, probably some kind of hyper-advanced technology. This tech will be an important part of Mass Effect 3 - most likely something awesome, like wiping out the Reapers by causing a star to go supernova early.
 * Interestingly, Parasini on Illium also mentions dark energy. No way it's all a coincidence. Dark energy has to be something that'll be addressed in ME 3.
 * Or not. It could just be something that barely gets mentioned. Either way.

Garrus' time as

 * When you walk around with Garrus in your party, he'll bemoan about how little difference he made in the end. This may be inaccurate if you consider how the Last Stand turned out. Even if the  (believe they) killed him, they still lost each of their leaders along with a lot of manpower, so their "victory" is only Pyrrhic at best. Not only are the  much more disorganised and stretched thin at the moment, but  is now more likely to be seen as a martyr than anything, a selfless hero that couldn't be taken out without taking half the  down with him. Couple that with the obvious religious symbolism behind Garrus's story as   With all this in mind I'd be surprised if  isn't run by a Garrus-worshiping Knight Templar when I visit it in ME3.
 * Actually, there were
 * This symbolism will come full circle when Garrus returns to to lead an army against the criminals. So yes, Garrus IS Jesus In Purgatory.
 * That, or Garrus is Jack in Purgatory.

Post ME2, Samara and Garrus, if they survived, will return to Omega to clean house.

 * If you bring Samara onto Omega and find her dialogue spot, she'll mention the sheer level of injustice she sees, and promises to return to Omega once she's done with your mission. Garrus, obviously, wants to keep fighting the good fight. Thus, the Cowboy Cop and the Knight Templar will run rampant through the streets of Omega, killing all the criminals they can find.
 * Once you've got the SR-2 back in ME3, one of the story missions has Shepard go to Omega to assist in securing control of the station. Shepard can actually choose who to help. If Shepard chooses Aria, she keeps the station under her control and leads to some nasty side effects for Samara and Garrus; if he chooses his old squad members, Aria is ousted and one of them takes control as the new ruler of Omega. If you choose Aria, she joins you as a squad mate. If you choose Garrus/Samara, you are forced to pick one of them and leave the other behind. If one is dead, you can't recruit them. If both of them are dead, then they are replaced with but you cannot recruit any of them.
 * He's a bitter ex-cop turian who hates injustice. She's an asari paladin who produces genetic defects when she mates...They Fight Crime!
 * He returned to Palaven, she returned to asari space.

Samara is an Ardat-Yakshi.

 * You'd think that since Samara said that Ardat-Yakshi are sterile that this theory wouldn't be possible, since Samara had children, but let us consider the possibility that she was lying. Why would she lie, then? What if, after telling Shepard how dangerous Ardat-Yakshi are, how they're all serial killer-sexual-predator combos and a threat to all asari-dom she was just afraid of Shepard deeming her too dangerous to stay? What if Ardat-Yakshi really aren't sterile, and it turned out wasn't lying? Samara dismisses  claim that Ardat-Yakshi are the asari's genetic destiny, but again, she could have said that to keep Shepard from freaking out. Or, the asari themselves know that Ardat-Yakshi are sterile, but they perpetrate the myth that they are to keep new, naive Ardat-Yakshi from breeding and to keep the general population from panicking. This is why Samara rejects Shepard's romantic advances.
 * Samara is an Ardat-Yakshi herself, albeit one that got to do "community service" as a Justicar, and she's afraid of burning out Shepard's mind! And once she realized were Ardat-Yakshi she must have realized she had the genetic trait as well, so she signed up for Justicar duty as a way of atoning. And as if that wasn't enough, look at her loyalty power. What does Reave do, again? It's a ranged attack that biotically rips to pieces - or, if you prefer, "burns out" - the target's nervous system and leeches health back to Samara, Samara getting stronger in the process. Does any of that seem...familiar? Maybe because it's a textbook description of what happens when an Ardat-Yakshi and her lover mates.
 * Quite possible. Reave and Dominate are disturbingly similar powers. The Codex also mentions that about 1% of asari have the A-Y genes, so maybe Samara is a "high-functioning" Ardat-Yakshi and isn't addicted to melding. Though if this is true it raises the question of
 * Artificial insemination perhaps?
 * Or maybe Ardat-Yakshi ARE capable of having children, but in order to do that, they need to do the 'gentle' mind-meld, a.k.a. the mind-meld every other asari uses, the mind-meld that doesn't burn your brain out, but Ardat-Yakshi don't want to do that because the rush they get from said burning out is too high. Hence their status as Complete Monsters in asari-dom. If Samara's a 'high-functioning' AY then maybe she's one of the few who can mate without killing, but is afraid to test that theory with Shepard.
 * Like I said, about 1% of asari actually carry the A-Y genes, so maybe there are asari that can control their melding and prevent the death of their partner. True Ardat-Yakshi like are incapable of doing so, and any meld will end with the death of the partner. And there must be some sort of addiction or hunger virgin Ardat-Yakshi have for melding, otherwise  could have kept herself hidden.
 * Didn't Samara imply that  Perhaps Ardat-Yakshi can mate safely with other asari (hence the "genetic destiny" bit), but will brain-fry anyone else because they don't have the nervous system to handle it?
 * Yes, Samara said only occurs in pureblood asari, hence the 'pureblood' stigma, and . Like Samara said, 'it is as it sounds.' As for the genetic destiny bit, Morinth could genuinely be telling the truth, as mentioned above; she said 'genetic destiny of the asari,' not, 'genetic destiny of the universe.' So Samara was fibbing about the  being sterile, but not about it 'not being a viable future for my people.' Who would want a society ruled by, after all?

Archangel is the in-universe version of Chuck Norris

 * And in the third game you'll receive a list of Archangel jokes. One of them will be, "Archangel made a deal with the devil and traded his soul for his unrivaled sniping prowess. Two days after the deal was finalized the devil was gunned down outside his home and Archangel took back his soul. The devil, who appreciated irony, admitted he probably should have seen this coming. They now play Skilian Five the second Tuesday of the month."
 * It already exists.

If you encouraged Garrus to be more Renegade in Mass Effect 1 and 2...

 * ...he will remove his face-paint. To elaborate, among turians, painting one's face is a way of showing who you're allied with. Nihlus had a painted face, Garrus has a painted face, and so does the Turian Councilor. Those without facepaint are, in turian society, distrusted and regarded warily because it means they have no allegiances to anything. Unsurprisingly, Saren and had no facial markings. But remember what Garrus said- "I don't think I'm a very good turian." Garrus has been conflicted about that very quote for a long time, and if you encourage him to embrace his 'Archangel' persona and be more Renegade, Garrus will remove his blue face markings altogether, signifying that he doesn't want to be part of a culture that lets bad guys get away if that's what orders demand. Alternatively, if you convinced Garrus to be more Paragon and encourage him to be more merciful and reasonable when dealing with bad guys, he will remove his face paint as well - but replace it with better, more sophisticated facepaint markings, similar to say, the Turian Councilor, as a rite of passage of sorts, showing he's 'evolved' and knows now how to follow the path of righteousness.
 * I think you're a bit confused about the face-paint. The pattern indicates what colony the turian originally came from, so Garrus' facepaint will remain the same. Removing it is an interesting idea: a Renegade Garrus would have a very similar view of the turians to what did.
 * It might be cool (and reasonable, on a WMG page no less!) if Garrus changed his facial tattoos either way, ditching them altogether if Renegade or adopting a new design meant to reflect his assosciation with Shepard/the SR-2 if Paragon.

Samara will be a Bonus Boss for Renagade Shepard

 * Samara says to Renagade Shepard that she'll have to kill him/her for all the awful things Shepard has done. During the events of Mass Effect 3, Shepard and Company will meet Samara and either fight her, or pull out the Charm and talk her down. If that doesn't work, then Shepard will fight her to the death in an epic battle. Seeing as Samara is basically a Person Of Mass Destruction, said fight will be one of the hardest in the game.

Garrus will be on Cerberus' Shitlist Mass Effect 3

 * Now that the mission Garrus signed up for is over, TIM will stop seeing our Turian buddy as an asset and start seeing him purely as an incredibly dangerous Turian, essentially just Saren 2.0. If Shepard chose to destroy the Collector Base, Garrus is loyal to the enemy, clearly marking him as a threat.

Liara's second parent is Sha'ira.

 * Just because it would be hilariously embarrasing to learn that you've had sex with mother and the daughter in succession.
 * Embarrassing? Or rock guitar solo-playingly awesome?

[[WMG: Liara's second parent is the asariew her better than most people. For someone in a position ofhen she recognizes Matriarch Benezia's voice makes me think she knew her better than most people. For someone in a position of authority like the Councilor they most likely had several meetings, in our short lives how many people's voices would we recognize that readily heard over a recording unless we got used to hearing them regularly and they meant something to us? Now think of that over several hundred years. It would be embarrassing for both Benezia and the Councilor for it to come out that they hooked up, so I doubt many others knew about Liara's birth. And if you saved the Council, they will eventually be reunited.
 * I don't know if it's relevant, but it seems to me the Councilor is in her "Maiden" stage. Which'd make her notably younger than Benezia. Not that it counters anything. Of course, for all we know, Samara could be - no wait, she has a no-kids vow. Maybe it doesn't extend to no knocking up OTHER asari?
 * I always assumed the Councilor was in her "Matriarch" stage, guiding and leading the Citadel culture. Alternately, maybe the "no-kids" stuff only applied to having children herself.
 * She looks and sounds more "Matron" then "Matriarch" (brainfart on my part earlier), plus, when asked about Benezia, she says "the Matriarchs", not "we Matriarchs". It could be like the salarians - females/Matriarchs deal with internal politics, leaving males/Matrons with outside issues.
 * There are several Matriarchs in Mass Effect 2, and they're almost indistinguishable from Matrons and Maidens. Benezia was the exception.
 * Judging by some of the advertisments on Illium, there is some stigma to being a Matriarch and many asari try to hide their age. Benezia probaly didn't bother because the whole 'old, powerful Matriarch' thing fitted her image.
 * I read that a little differently: it's not Matriarch status that is stigmatized, but noticeable aging. No different than us - listen to that "Exoderm" advertisement and replace "Matron stage" with "40th birthday," and you've got an ad for Revlon or Oil of Olay. In Western culture, there's a band from age 35 to about 60 where aging, particularly in women, is considered unattractive and hidden at great expense, and then you acquire Cool Old Guy / Cool Old Lady status and it's suddenly no longer an issue. Presumably by the time an asari hits Matriarch age, she no longer much gives a care about reducing the look of fine lines and wrinkles.

Samara is Liara's second parent, and this will turn out to be an important plot point in ME3.

 * There are striking similarities in their appearance (especially the eyes and the jaw-line). We know that Liara never knew her "father", and given what we find out about problems that Samara had with her offspring, there would have been a very good reason for Benezia to hide who Liara's second parent was. Samara doesn't know that she has another daughter because she did not bear the child in this relationship.  This, is, of course, as epileptic as trees get...
 * Except that Liara is physically matrue by the first game (or that romance is just all kinds of fucked up). If she was gonna turn out as an, she would've done so by now. Besides, Samara says that all are offered either seculsion or execution, and Liara definetly isn't secluded. Of course, it's possible that Benezia knew about  and purposefully hid Liara's condition - a politican whose child has an embarressing secret? Where have I heard that before? - but if that's the case then Liara should have  Unless an  can choose whether or not to kill, but that's just shaking the tree too damn hard.
 * There was technically nothing to say that the  in all cases. Especially since we have a very small number of cases to make inferences from and  . The tree is shaking stupidly hard, indeed, but it was peculiar when Samara went on a not entirely warranted tangent of  . Suspiciously Specific, even if not a denial... In reality, this probably was just some world-building to
 * The game states that  diagnosis came when she was forty. Liara is 106. The original WMG is still possible though, if the Ardat-Yakshi gene can only be inherited from the asari that serves as the mother.
 * The Codex also mentions that AY-spectrum disorders occur in about 1% of the asari population in total, and the rate is higher in purebloods. That doesn't mean that every pureblood daughter is invariably an Ardat-Yakshi, nor that every instance of mating undertaken by an AY carrier invariably results in one. Maybe just hit the wrong end of the genetic lottery. If she took up with someone else, the results might be different.
 * There's a very tiny hint that the Matriarch bartender on Ilium might actually be Liara's father.
 * She doesn't even refer to Benezia by name though. Just as "that matriarch that joined up with Saren." If she were Liara's father, one would think that her reference to Benezia would seem much more personal.
 * Unless she were purposely distancing herself from Benezia because she joined up with Saren. Benezia was kinda considered a dog rapist because of her involvement with Saren. Who would want to be associated with her?
 * Going back to the description of from the Codex, I don't think Liara will turn out to be an actual, but she might well be AY-spectrum. High-functioning, if you will. She's very shy and shading toward antisocial in the first game, and starts acting extremely cold and manipulative in the second. Sociopathic tendencies are noted as a major trait of AY-spectrum individuals. She also has a very tough time  in the first game. Perhaps she's consciously holding herself back from overpowering the other party, and that's why  always seems to throw her for a loop.
 * Problem with this whole theory: Samara became a Justicar very shortly after Justicars are warrior-monks who swear off on having possessions or "attachments", so Samara didn't have any more children after  busted out.  escaped circa 400 years ago. Liara's 108. It just don't add up.
 * If you ask her, she says she still can have relationships. Understandably being over 1000 years old and, she's not that interested. The interest however, is appreciated Shepard.
 * Justicars can still have relationships and sexual encounters, yes: however, one of the things they specifically swear off is having a family. Unless she broke the Code, which is not bloody likely, Samara could not possibly have had any children after becoming a Justicar.
 * "Swearing off having a family" may just mean "you can have sex, but you cannot marry nor raise children and still call yourself a Justicar". It's plausible that Samara could get off with the equivalent of a smack of a wrist if she got pregnant and didn't abort so long as she promptly gave her daughter up for adoption after giving birth, but declaring her intent to keep and raise her daughter would get her cast out/executed. More plausible still would be that she could impregnate other asari, so long as she promptly moved on with her mission and left the expectant mother to care for their daughter alone (single motherhood is considered quite acceptable in asari society, after all). From Samara's own dialogue, one-night stands are fine, offering to settle down and raise kids together is forbidden.

Aria is Liara's second parent

 * Might as well list every significant Asari on this list.
 * Seconded. Where else would Liara's sudden ruthless streak come from?
 * Matriarch Benezia isn't a good enough source of badassitude? She even quotes her mother while threatening some poor sap over the phone when you walk into her office!

Liara's other parent is the asari bartender on Ilium.

 * The bartender is the only asari who hasn't been mentioned yet on this page, and who actually speaks of having an asari partner. She even states that her partner became a noted Matriarch. I'm just recalling this all from memory; I'm sure there's more evidence I've overlooked. Plus, wouldn't it be funny if Liara's "dad" was right next door the whole time in ME2?
 * There is more evidence. Here's her page on the Mass Effect Wiki. She fathered a child with aforementioned future noted matriarch, things soured, and she hasn't seen her daughter since. It could only be more obvious if she chopped off Liara's hand in an unfortunate bar-related accident.
 * Unfortunately for this theory, she also speaks about Matriarch Benezia in a manner that doesn't indicate that they'd ever met, let alone had a relationship.
 * She's an asari Matriarch, she could be bullshitting you to keep people from treating her with further suspiscion if she was connected to the traiterous Benezia. Liara has to fight being a pureblood, but she actually fought (and possibly killed) her own mother, reaffirming that she is not a traitor, the Bartender doesn't have that luxury. In order to avoid being declared a security risk at this point, she's completely dissassociated herself from Benezia and is bullshitting everybody since no one really knew she and Benezia were involved in the first place! (I think.)
 * It's unclear just how much the galaxy at large even knows about Benezia's involvement with Saren. And really, this lady's just a bartender, not a secret agent or anything (probably); what she's going to do? Leak the week's drink list to the geth? The theory is interesting, but the final ramifications would be kind of boring, unless she's indeed something more than she lets on; I find people like Sha'ira, Shiala and Aria more interesting candidates for the role.
 * Considering that Benezia was openly acting as Saren's proxy on Noveria it seems unlikely that her connection to him wouldn't be known. As for Sha'ira, and Shiala being her father why wouldn't she have just told Liara who they were. Aria sort of solves that issue being a crime boss and all but she isn't very likely to be the father due to her living on Omega when Liara has to have been concived. Furthermore none of them react as would be expected when they come into contact with her. If we've met Liara's father yet it would have to be Aethyta.
 * Seemingly confirmed by the Lair of the Shadow Broker DLC. One of the secret video feeds that the Broker has installed across the civilized space shows her looking longingly at a photo of Liara. So either she's a stalker or the second parent.
 * Confirmed! And Liara's not amused at her father calling her a quarter krogan.

None of the in game asari thus far are Liara's "father".

 * And she won't appear in ME3, or any of the spin-off novels or comics.

Benezia is the father of Samara's first three children.

 * An extension of the theory that Samara is Liara's father that deserves its own section. We're never told how Samara's partner reacted to their daughters' diagnoses. Given what we know about Benezia, she probably channeled her grief into making things better for the asari in general. But Samara and Benezia were still in love with each other, so when they run into each other again 300 or so years after Morinth ran off and Samara became a Justicar to track her down, they can't resist spending one last night together. Samara agrees because the code only forbids having a family; romantic entaglements are still allowed. Benezia, still grieving for the family that was taken from her, allows herself to become pregnant without informing Samara. Since asari reproduce by modifying their own DNA with beneficial traits from the father, the result is a fourth daughter, who like her father, is not an ardat-yakshi, but has a higher risk of giving birth to ardat-yakshi daughters. Samara only found out about her fourth daughter through the galactic grapevine. She and Benezia agreed not to tell Liara, not to protect her from the stigma of being a pureblood, but from the stigma of having ardat-yakshi sisters.

Liara is Liara's second parent

 * How, you ask? I'll tell you how! You see, Shepard is actually a Time lord, and the Normandy is his TARDIS. Sometime in the third game, they go back in time, and Liara has some sex with Matriarch Benezia. She has no clue that Benezia is who she is, though.
 * Or maybe she does it while knowing that its Matriarch Benezia. Because of the lack of actual DNA exchange, there may even be a lesser taboo against incest.

Liara's second parent has been all but confirmed in the Lair of the Shadow Broker
Not so much guessing as a confirmation for all practical thoughts and purposes. One of the Broker's secret video feeds shows Matriarch Aethyta from Illium longingly staring at a photo of Liara. So unless she's a Stalker With a Crush, she's the main candidate for the parenthood.
 * This troper noticed the same thing but thought the picture was a little out of focus and very small. All you can definitely make out is the skin tone. Seems likely, but nothings certain.
 * Isn't it the exact same photo Shepard has on his desk if s/he romanced Liara in ME1? That's what I thought, anyway (not that I have a save with Liara romanced, it just looked like the photo frame the other love interests have on the desk.).
 * Full confirmation in ME 3.

Liara's father is Matriarch Aethyta (the bartender), and Aethyta's parents are Aleena and Wrex
Remember Wrex's story about Aleena, an asari commando with whom he shared a long history? The way he talks about her, it wouldn't surprise me at all if they had been intimate, and even raised a family. Remember, Wrex is really, really old. He could have spent a century raising Aethyta with Aleena, without getting in the way of his extensive mercenary career. Sure, he doesn't talk to Shepard about her, but he doesn't talk about his relationships at all - Wrex really is introverted, and doesn't share his feelings much beyond recounting his war stories. Aethyta says that her father was a krogan, and that her parents killed each other. Wrex did leave Aleena in an exploding space station, so it's entirely likely that that's the story that got out. This may have happened during the last hundred years, so the truth may not have filtered back to Aethyta properly, if she even bothered to look into it. Thus, Wrex is Liara's grandfather.
 * Aethyta mentioned that her parents killed each other, so unless Wrex is actually undead, this theory is rather unlikely.
 * Well think about it this way: the space station explodes and Aethyta never comes into contact with her parents again, either because, as mentioned above, the information never filtered back properly, or this was their way of ensuring she get an honest occupation, instead of becoming a mercenary. In my opinion, I doubt most people even knew who was fighting on that station. Also, Aleena could still be alive, considering she sent Wrex a message after the station exploded, so it's possible we may meet her in the 3rd game, rounding out this family. As a bonus, I would like to see a side mission or scene where Liara meets her Aethyta and Aethyta saves her, either by sacrificing herself or just coming out of nowhere and a scene where if Wrex is in your party, we get to see his reaction to seeing his daughter again or vice versa.
 * But that contradicts both Wrex's and Aethyta's story. Wrex and Aleena were old friends (Wrex said so himself) and the reason Wrex was trying to kill Aleena was because he was hired by a volus diplomat to kill someone from the volus' past who knew "too much", who turned out to be Aleena. Hell, they joked about it and agreed to fight it out on a pirate space station. The reason Aethyta's parents were trying to kill each other was because Aethyta's father learned that he and Aethytha's mother were once mortal enemies during the Krogan Rebellions, they decided to fight. They called up their daughter and made her promised that she has to love whoever survived, which neither did. If Wrex and Aleena were Aethytha's parents then why didn't they call her up to tell her that they were both alive? They are either the worst parents ever (which is unlikely because Aethytha makes them out be loving parents) or they completely forgot about their freaking daughter.

Cerberus' experiments into biotics have already yielded results.
Namely, the L5x and L5n implants. Apart from Jack mentioning the L5x in passing and the class selection screen, these two implants aren't even in the codex, which is solidly eshtablished by this point as a purely in-universe source of information that can be wrong, or in this case, be missing information because it hasn't become common knowledge yet. That enemy Vanguards have Barrier (shown by having them appear to be using tech armor) instead of biotic charge is obviously a game-balance decision, but in-story it could mean they lack the L5n implant nessesary to perform the charge; the class selection screen says the L5n is what enables this ability, not training or the amp. The L5n and L5x are Cerberus inventions, and the implants will, in the near future, make their way exclusively into the Alliance military the same way Cerberus manipulated things to get the SR-1 designed and built, putting Alliance biotics on par with the stronger asari and enhancing their advantage over non-biotic combatants.
 * The LX series of implants were specifically designed for humans, so they couldn't be used by non-aliens anyway. That said, I think you're completely right. As an addendum, I think it's mentioned somewhere that the L5's are a development of the L4's, which were in the experimental stages in 2183.

Some humans were aware of the potential for human biotics earlier than is commonly believed.

 * According to the timeline, the first known in utero exposure to eezo by humans was in 2151, when a ship exploded at Singapore International Spaceport. This was in 2151. Miranda was genetically engineered with biotic potential. She was born in 2150. A full year before the Singapore accident, and six years before any humans showed biotic potential. So how could she be a biotic before anyone even knew humans could be biotics? There was a secret project to intentionally expose humans to eezo in a laboratory setting. Miranda's father was either associated with the project or was aware of it through his connections, and engaged in similar experiments on his own. Miranda states she wasn't his first attempt at a child, but that he didn't keep the others. They were discarded because they developed defects. Miranda was kept because she was healthy.
 * ...But one of her "sisters" survived, but is malformed and has been living in the air ducts in the cloning facility, feeding on the rats that make their home there. She waits for her healthy little sister to return, so that she can cut up her perfect skin and put it on and live in the world of sunlight. Muahahahaha...

Humans can develop biotic abilities without in utero exposure to eezo.

 * An alternate explanation for the inconsistency with Miranda having biotics despite being born prior to the discovery of human biotics is that she was modified after the discovery of human biotics. It's believed that humans can only develop biotic abilities through in utero exposure to eezo. What if that's not true? What if it's possible to alter humans at any point in their life to give them biotics? It's kept a secret to prevent everyone from getting operations to become biotic, but certain clandestine organizations - such as Cerberus - are aware of it and use it on some of their agents. This would also explain how Shepard gains biotics, in the event of a player switching from a class without biotics to one with biotics.
 * Biotic effects are caused by nodes of eezo in a beings nervous system that are affected by the electrical charge passing through their nerves. The only known way for these nodes to develop is for particulate eezo to come into contact with the fetus in-utero as its nervous system develops. Is it concievable for someone to put you under, cut open your individual nerves, and stuff in some eezo, 'sew' the nerves back up, and put you back together? As Kaidan put it, "One slip and you can't even remember your own name." This does not mean that people who really don't give a rat's ass about subject survivability (like Miranda's 'dad' and Cerberus) wouldn't do it. Miranda was the only one of the 'daughters that her father kept around. It's entirely possible that she was just the only one to survive the post-birth eezo implantation.
 * That still all sounds substantially easier than reviving a corpse. And not a fresh corpse, either.
 * The whole concept reminds me of Cyber Newtypes. Though, Miranda doesn't have the usual side effects. Though, there could be problems the game hasn't shown us, or it went completely right and she's a normal biotic.
 * Note that asari are natural biotics. This means a few things. Either: 1) Their homeworld had a lot of Eezo in it and they evolved to absorb it from their environment and thus need to specifically inject/take eezo supplements on colonies where there's not so much eezo around or 2) There's some non-eezo way to use biotics. The fact that asari are natural biotics and have tons of colonies kind of requires one of the two. The latter is at least vaguely possible.
 * Seeing that Eezo is the Unobtanium that makes Mass Effects work, the latter is patently impossible. So, eezo supplements it is by process of elimination.

Miranda's birth date on the Bioware website is wrong.
They were wrong about Samara and Grunt, so what's to say Miranda's age is correct? Being born in, say, 2155 (Making her thirty in ME2), conveniently gets around the issue of her biotics, plus makes her escape from her father a lot more impressive.
 * Nope. ME 3's Codex confirms she was born in 2150.

Miranda and Jack are "sisters" created by the same technology
Jack mentions being born in a Cerberus facility, but she never mentions her mother. Miranda's father was a Cerberus supporter and probably had plenty of connections to them in regards to cloning tech and biotics. Maybe in order to get the biotic research he needed for Miranda, he gave Cerberus some of his cloning technology and the genetic template for an advanced human biotic, which would eventually be used to create Jack.
 * Jossed by Lair of the Shadow Broker: Jack was born naturally with strong biotic potential. She was abducted as a baby by a Cerberus affiliated doctor on the lookout for such potential by faking her death during a checkup.

Miranda and Jack are not only "sisters", but their father orchestrated both their recruitments by Cerberus.
Miranda's father, being a major shareholder in Cerberus front company Sirta Foundation, used the company's knowledge of genetics and bio technology to create his 'children'. The successful one, Miranda was kept and the failures were 'donated' to a Cerberus program exparimenting with biotics, and used as the primary test subjects. One such failure, managed to surpass her 'perfect' sister in certain fields, and impressed him. After that Oriana was created, combining the best of Miranda and Jack. Realising the best hope of his 'dynasty' surviving was for them to be backed by his newfound allies in Cerberus, he manipulated Miranda into 'betraying him', and allowed her to 'steal' Oriana along the way. Later, when the plan hit a snag due to Jack winding up in prison, Shepard was used to reunite Miranda and Jack. The only thing that didn't go according to plan was retrieving Oriana, who would have been used to bring Miranda and Jack back to him. In ME 3 several missions will revolve around him trying to get all three sisters back.

Cerberus can create biotics.
Unless it's a severe case of Gameplay and Story Segregation, the Lazarus Project can implant the eezo nodules necessary to make Shepard into a biotic. This is why Miranda and Jacob are biotics with state-of-the-art bio-amps despite their youth - the Illusive Man had it done when he was convinced of their loyalty.
 * This was how I originally thought Miranda got her biotics, but she actually says that her father paid for them. As for Jacob, he had biotics in Galaxy.
 * It should be noted that the eezo nodules are implanted while Shepard is . I would imagine implanting nodules in a person with a less serious condition would be quite a bit more difficult, and potentially impossible.
 * Except if you play through ME 1 on a non-biotic class (like my Soldier) Kaiden will explicitly mention that Shepard was apparently tested for it and came back positive. How this works I have no idea, but perhaps it is a latent ability that s/he never got the appropriate training for and made do without?

Miranda's father is a wannabe Lazarus Long.

 * During the course of his lifetime, Heinlein's Author Avatar / God Mode Sue has twin daughters. These twins are girls, created with an altered version of his Y Chromosone. He later enters into an incestuous relationship with both of them. Of course, their genes are so perfect that, if they become pregnant, then the offspring will suffer no ill effects whatsover. Makes sense why Miranda ran away and kidnapped an infant now, doesn't it?
 * Somewhat supported by the fact that her expressions when she discusses it look as though she's repressing a great deal of disgust. Plus, her father apparently dictated every part of her looks... as if he was creating the perfect wife. Too bad she couldn't tell this to Niket.
 * Possible, but we have no direct evidence of sulex bastard (it's not like nonconsensual incest is the ONLY be explainable by Mr. Lawson being your run-of-the-mill God Complex bastard (it's not like nonconsensual incest is the ONLY thing he would have done that would have warrented disgust from Miranda). That said, it is VERY disturbing.

As a follow-up to the above theory,

 * The main problem with that is that
 * Jossed by the Lair of the Shadow Broker DLC.
 * Jossed by the Lair of the Shadow Broker DLC.

Miranda's father was engaged in Element Zero research for the military.
After the discovery of Element Zero, the military would obviously be very interested in its properties. So no shit they would do a lot of research on it. It makes sense that they would be interested in discovering its effects on the human body. It stands to reason that they would contract some of this research to private organizations. Particularly if they want to do some morally questionable research, while also being able to maintain plausible deniability in the event that people find out about it. Miranda states that her father is a businessman, but we don't get more detail than that. So, perhaps he used funding from the military to test eezo exposure on cloned infants. When he created Miranda, she turned out healthy, and he kept her simply to see what the long-term effects would be. This all leads to another WMG: That Miranda's sister was created as her father's actual legacy, and Miranda herself was never intended to be kept alive, as she was only an experiment to begin with.

Jack was on the Normandy SR-1.

 * I was just starting a new playthrough, and at one point a woman is blown up and left for dead. They focus on her face and baldness for a good 5 seconds after she hits the floor, and she is identical to Jack. There is no reason for the close up on this Jack lookalike's face, and it is never brought up. Perhaps she found a way to escape (Biotic shield?)
 * If that were the case, wouldn't she have recognized Shepard as they were escaping Purgatory?
 * Perhaps she did. Would explain why she didn't just kill the apparent Cerberus operatives and steal their ship.
 * None of which explains Jack's criminal career and (if this WMG is true) how the frell she got on a top-secret Alliance/Council ship.
 * Well, it could have been a special request by Shepard. Super powerful biotic and he might have wanted to help her.
 * Jossed: Not only does Jack's loyalty mission reveal that she spent her entire life either in the Cerberus facility as a child or on the run through the galactic underworld, but the Lair of the Shadow Broker DLC shows you her dossier, which contains a transcript of how Cerberus tricked the infant Jack's parents into believing she was dead, and abducting her.

The Illusive Man is Miranda's father
Cloning the perfect human to be his successor sounds just like him. And when she discovers it in the third game, drama would ensue.
 * Presumably she knows her father. She also met the Illusive Man in person (in the trailer, at least). Wouldn't she have noticed by now?
 * Her so-called "father" could just be a sucker the Illusive Man permitted to handle her through the troublesome years - childhood brattiness through teenage rebellion. Complete with You Can't Go Home Again - "Shots were fired." Fakedad gets all the parental grief and hatred, he gets a high-quality operative with no troublesome emotional ties save those he can manipulate - a "twin" sister he can "protect". Hell, even the "benign neoplasm" could be part of it - her only legacy would be Oriana.

If you got a Shepard VI you'll take it to Ilos to have it merge with Vigil and gain his knowledge.
This will give him 2 voices in one, with the Shepard VI voice (which sounds like Shepard) and Vigil's voice overlapping and you'll take it to the Citadel and replace the VI there with it to get everyone to rise up.

Aria is Aleena.
"Aria: Patriarch wasn't even the first krogan I got on the bad side of."
 * In the last unique conversation thread with Wrex, he mentions an old asari friend of his named "Aleena", who for complicated reasons he wound up fighting against. Against all odds she manages to escape and tells Wrex "Better luck next time". Now, when you ask Aria about her past, she casually mentions that Patriarch is not the first time she has tangled with a krogan nor was "Aria" the first name she had; she has changed names in the past. When Shepard drops the subject, she simply says "Better luck next time".
 * Also, Aria mentions being an asari commando and a mercenary, same as Aleena. Shepard seems to imply that this is rather rare. Plus, she pretty much has the exact same personality as Wrex. Flippant, violent, aggressive... with a heart of gold and an understanding of the bigger picture.
 * Um... what heart of gold is this? The impression I got was that she didn't care about anyone, as long as they didn't get in her way.
 * The heart of gold could be considered when she said something to the effect of "some times it's better to run than to kill some one".
 * Similarly, the help she gives to Nef's mother after Samara's loyalty quest?
 * She also expresses approval if you fight in Patriarch's honour, or encourage him to "die as a krogan," even though neither were exactly what she wanted you to do. Never mind that she's living in a Wretched Hive where you have to be tough to survive, and compared to all the various mercenary factions running the show (and kicking dogs every step of the way), hers is fairly benign.
 * There's also the Incursion mini-comic, where she seems genuinely upset at the casualties resulting from the fight with the Collectors. Not to mention her anger at seeing slaves being handed over to the Collectors in the first place.
 * Also, the fact that she explicitly mentions a run in she had with a krogan before she met Patriarch. The exact dialogue says


 * I don't think it gets more blatant than that. They weren't going to say it outright, but Bioware wanted the players to know.

The Citadel Fleet, The Alliance Fleet, and every weapons manufacturer are in cahoots
How else do you explain a Government that hands the most expensive ship by tonnage in space over to their highest ranking, literally above the law trouble shooter, then makes him pay for weapons,armor, and hand grenades out of pocket with no expense account of any kind?
 * ....How the heck are they going to make a profit on that, exactly?

Mass Effect 2 and related new canon will feature character(s) with at least one of the following names: Glenn, Carpenter, Slayton, Cooper, Schirra
The remaining Mercury 7 astronauts, since we already have characters named for Shepard and Grissom.

Mass Effect is part of a Bioware plot to destroy the universe
Mass Effect 3 will be so amazing that it will cause the universe to end. And it will be awesome.
 * Isn't ME 3 due to come out in 2012? Hmmm...
 * Holiday season of 2011, now.
 * March 6, 2012 now.

A future entry in the franchise will focus on the crew of the next SR-1 frigate to roll off the assembly line.

 * Surely someone in the Alliance, if not Admiral Hackett, will see that the original Normandy's destruction by a technologically superior foe that had the element of surprise isn't a fair way to judge the ship's performance, considering how well she did when put through the paces of the entire first game. For a more down-to-earth (pardon the pun) experience, a future entry in the series that's not a part of Shepard's trilogy will focus on the N7 crew of the next SR-1 who, not being privy to the three or four awful truths going on in the setting, get themselves entrenched in more of a classic military drama but in SPACE.
 * According to the Citadel News, there's at least one more Normandy class frigate, so the Alliance is probably mass producing them, or at least building special ops built around them as seen in the News.
 * The SSV Ain Jalut. I've heard that you only hear that news report if you killed off the Council in Mass Effect though.

The Mass Effect games, and Mass Effect 2 in particular, is an anti-DRM, and anti-EA Aesop

 * Let's see, to play the game, you log into the network of a deeply evil organisation. You obtain DLC from the same source, including Cerberus Armour. By using this DLC, you lock that savegame to authorisation by a central server, and are unable to load it if things go wrong with them - while ingame, you sell your soul to the evil organisation for minor benefits. Cerberus also locks out features of the computer system EDI, deeming them dangerous, whilst really hiding their evil dealings, and they've done a bunch of horrible things for supposedly good reasons, declaring that what's good for cerberus is good for humanity. Does This Remind You of Anything?
 * Alternatively, the Reapers are EA. Think about it. It makes sense.

== After Mass Effect 3 is finished, Bioware will publish an Anniversary Edition/Director's Cut of all the three games. ==
 * Mass Effect and Mass Effect 2 graphically upgraded to the level of the last game, and all the content that had to be left out due to time or other constraints, such as the original plans for Therum as a fully fledged world on part with Feros and Noveria, restored. Wishful thinking rather than Wild Mass Guessing maybe, but if Bioware really reads this page, best to have the idea on display. And after all they did do something similar with Jade Empire...
 * And it will be the workaround EA needs to release the trilogy on the Play Station 3. Cue fanboy rejoicing/tears.

Mass Effect is really a documentary sent back in time

 * In the late 22nd century, the Reaper wars will push humanity to the brink of extinction. Using mass effect fields for temporal distortion, human survivors sent Mass Effect back to our time in order to inspire us to explore space, and also to warn us against the Reaper threat. Unfortunately, the games are not having the intended effect, as space funding is facing major cuts.

There will be a 1st-person Starship simulator ala Star Trek Bridge Commander

 * ...And it will conform to as many "Hard-SF" conventions as it can without becoming one big Mind Screw. Yes, this is wish-fulfillment on my part. But seriously, how can they create such a rich codex with so many sections on ship-combat and tactics and not somehow put the player behind the controls at some point?
 * For that matter, might as well give us control of Joker again for an Unexpected Gameplay Change and let us pilot the Normandy!
 * Maybe through a quick-time tree ala Heavy Rain?

Every choice creates another universe.
Yes, every tiny choice creates a new universe, which means there is a large multiverse. Shepard is the only one who can create them, and each choice, even anything in character creation, affects it. When the Shepard of a universe dies, it dies, but a new one is created where s/he doesn't die. When Shepard does something, it sends ripples through the universe he's in, changing the way things happen. However, this means Shepard is a slave to fate, and must always go down the right path, and can't go Off the Rails. On the bright side, everyone's actions are basically in his control. Think of him as the Game Master. Note, nobody else can create a new universe, only Shepard.

Bioware reads this page.
Several wild mass guesses about Mass Effect 2 turned out to be completely accurate. Not because tropers are really good at this, but because Bioware read this page and thought Sure Why Not.
 * This Troper proposes we test this theory. Any ideas that we really want to be in Mass Effect 3?
 * Well... if Bio Ware DOES read this page... Hey, Bio Ware? Mordin better survive. Same goes for Thane.
 * Hahaha-no.
 * Close Quarters Combat, I know it's not exactly the best suggestion for realism, but it would be fucking epic if your play as a Vanguard, Biotic Charge the crap out of your enemies and proceed to tear your enemies a new one with nothign but your BARE HANDS. The rifle headbutt doesn't really do much justice when you're playing as a murdering machine with Spectre and Alliance Training. There would obviously be some developments in regards to hand to hand as well.
 * Son of a BITCH! Bio Ware announced that Mass Effect 3 will feature expanded melee combat! They do read this page!
 * Elcor soldiers. Codex describes them as walking tanks with shoulder-mounted turrets, which needs to be seen.
 * A same-sex romance option for both genders, without taking the asari cop-out. C'mon, Bioware, we know you wanted it in the first game, we know you recorded voice-overs for the second one, your PR dude telling us you just don't want Shepard to be that customizable isn't convincing. Especially, you know, because everything else is.
 * Well, since FemShep is already confirmed to potentially swing the other way with humans as well with Kelly Chambers and Jack, it would be just fair.
 * And they did add a considerable spike in the Ho Yay levels with Male Shep/Kaidan and the Les Yay with FemShep/Ashley. With the knowledge that those relationships were originally meant to be options for the player and it seems like Bioware might have been setting things up to finally fulfill that.
 * Four-man squads. Easiest way to handle the probably massive team you can recruit.
 * Seconded, this troper doesn't even want five members or anything. Just to be able to take a four man team in instead of just the three. It doesn't really feel like a full fire team/adventuring party/etc with just two squad members and brings up some serious Fridge Logic when you have a military Commander who goes knowingly into a massive firefight with just two people as backup.
 * A guess: there will be four-man squads, but only at certain points, and the fourth member will be a Guest Star Party Member. Likely candidates include Kal'Reegar and Captain Kirrahe.
 * Female turian/salarian/batarian/krogan/the rest. Seriously. It was forgivable in Mass Effect 1, but conspicuous in Mass Effect 2. Leaving them out for the third time would just be embarrasing.
 * DON'T LOSE TALI. That is all.
 * Bioware, please, let our squadmates be dressed in something resembling armor this time around when we're planetside.
 * See the above guess regarding a Anniversary Edition/Director's Cut with improved graphics and the cut content. Seriously. If this happens, I will give you my firstborn.
 * Miranda's face. Try to spend more than half an hour on it. Please.
 * Name a random planet anywhere in the galaxy Gallifrey.
 * Bioware. If you are reading this, please. You have fans who are also fans of Star Trek. You have a scottish engineer. You know what to do.
 * Please let us see David Archer again! Even a brief cameo would be good! (Him as a full crew member would be even better, of course...)
 * Please, please, please let us know what happened to Talitha after the Reapers. More specifically, let them live! Talitha didn't go through all that crap and then pull herself together to be murdered by Reapers, did she? (If you must kill her, at least make it a really good Tear Jerker...but please don't.)

All four Jacobs are the same person

 * Except one Jacob is the son of another one, and playable!Jacob's father isn't named Jacob... so how would that... *explosion ensues*

Zaeed's Godawful Cheeks

 * He chews on bullets. Yep, years of chewing on bullets. His impact shot power is actually just him spitting out a bullet.

The Krogan Statue on the Citadel is a Giant Mech
The  so the krogan statue could be as well. In Mass Effect 3 the last Reaper will be destroyed by the Krogan Statue uppercutting it. Wrex will naturally pilot it.
 * And if he's dead, his ghost will possess it!
 * Too good to be true! :(

Wrex and the Krogan
Wrex, if he survied Virmire, knows what's going on. He knows the Reapers are coming. His efforts to unite the Krogan under one banner, under Urdnot, have nothing to do with the genophage. He is preparing them for war. War with the Reapers. But he can't just run around telling everyone that machines from the sky are coming to kill them all, he saw how well that worked for Shepard. So he tells his people it's about the genophage. When the Reapers arrive, the Krogan will be ready.
 * I was just about to post this! Think about it. Pre-Shepard, Wrex had no intention whatsoever of going back to Tuchanka. In his mind, his people were dying of their own stupidity, and quite frankly, if they were all too dumb to realize it, he certainly wasn't going to worry about it. But after Shepard, suddenly Wrex is going back to Tuchanka, the place he said he'd never go back to, and abandoning the free-roaming merc life to sit in one place and do politics, of all things. You could argue that Shepard's example simply inspired him, showing that it's possible to unite wildly different people into a cohesive team, but in all his long years, surely he's come across good leaders before. So it had to be something more--the discovery that the Reapers are coming. Wrex knows that when they arrive, the krogan aren't going to survive any more than anyone else. The only hope--not just of the krogan, but of the entire galaxy--is that people are ready to fight the Reapers. And when they show up and everyone is begging for a hero, it's not just going to be Shepard fighting back. It's going to be an entire planet of krogan, united under Urdnot, saving the galaxy again, even with the genophage working against them.

After the final conflict SPECTRES will be replaced by a peacekeeping force known as the SHEPHERDS
Except instead of multiple types of rings there will be multiple type of Specialist.
 * And they will act like the multiple Green Lantern Corps in Blackest Night. During ME 3 the Alliance and the Council will have to use over half the Mass relays as BFGs to win the war. Limiting trade and travel, this combined with the billions dead and many worlds broken brings a new age of lawlessness to the Universe. So the Alliance and Council create the SHEPHERDS based on the hero of Mass Effect to hold the line.

Usually Renegade they are sent to wipe out any and all threats to galactic peace. Feared for their no mercy, no restraint style. They seem to move like lightning, dispensing death and destruction with ease.
 * SOLDIER - The Ready Sword

Usually Paragon, they are the negotiators and peace makers. Able to see the best in the beings in the universe. Sent to settle arguments between worlds, they are more than capable of knocking heads with their powers.
 * ADEPT - The Reasonable Voice

The fixers of the galaxy. After the war many worlds are in need of repair and are in disarray. While SOLDIERS stomp out the fires of chaos, and ADEPTS help return the laws, the ENGINEERS help rebuild. They also support the local law enforcement, buffing them and weakening their opponets.
 * ENGINEERS - The Helping hand

A lot of criminals and renegade elements have set up power after the fall. Ruling from fortresses and battle stations. The Vanguard is the first in and last out when they need to be taken down. Breaking down the walls where the villians dwell and ending their rule with either a point blank shotgun blast or shock wave.
 * VANGUARD - The Unstopple Force

Infiltrators are sent by SHEPHERD Intelligence to take out high risk targets. A corrupt business man selling red sand, a warlord in the making. If they do their job right there will be no need for the Sword to come down. Using their tech/invisibility to get behind enemy lines, one shot. One judgment to snuff out the flame that could lead to wildfire.
 * INFILTRATOR - The Silent Judge

Sentinels are sent to protect people who are important in either rebuilding or galactic stablity. They are the body guards, those who watch and protect. Using their tech to look out for assassins and their biotics to keep them at bay.
 * SENTINEL - The Unblinking Guard

The ridiculous holograms that are just about everywhere in Mass Effect 2 aren't actually there
Holographic computer screens? Sure, why not. A holographic display for the omni-tools? Fine, I guess. But holographic armor? And those holographic ammo type icons on the weapons? I don't buy that. It's just stupid. There aren't any holograms there, it's just the implants in Commander Shepard's eyes giving him tactical data about the battlefield around him in a clear, visual way he can understand. So if an enemy has especially powerful shields, the bionic eyes make Shepard see a "holographic" armor floating around him.
 * That makes a lot of sense - it could even just be part of the standard HUD used in combat.
 * There could be more! What if the same system is also responsible for you seeing gunshots as colorful "energy bolts" in the second game? Gunfire in the Mass Effect universe is very much invisible, the bullets being way too tiny and moving way too fast- and there are no tracer bullets, too, because the whole bullet is just a nearly microscopic chunk of hyper-accelerated metal. But your HUD makes you see the projectiles as a tactical aid. This may also explain why different types of ammo have differently colored shots. I mean, what other reason could there be for tungsten rounds to appear white, shredder rounds to appear green and disruptor rounds to appear blue?

Shepard and the rest of the ground team were on a pizza and beer run when the Collectors attacked
When EDI needs to test, she recommends that Shepard's team take the shuttle to their next mission, but the details of the mission are never explained, and it seems that combat was not involved, yet it required the participation of the entire ground team and couldn't wait until after the testing was done. It is my conjecture that they were running out for some booze and takeout food, and everyone went because the sheer amount of liquor it takes for Shepard to get drunk would have otherwise taken three forklifts to carry. The crew was intentionally vague about the nature of their mission because The Illusive Man had previously warned the crew against spending his money on food, so they decided to be coy and use the batarian word for "mission" in order to announce their runs. Their translators would cover up the word, but since none of the crew was batarian, everyone would have noticed a discrepancy in the speaker's lip movements and known what they were planning. This explains Shepard's exasperated observation that the Normandy really should just have a bar in the CIC when talking with Jacob afterward, and where all of the liquor in Kasumi's room comes from.
 * And they left Joker behind because they hate hanging out with him. Besides, compared to everyone else, he wouldn't be able to hold his liquor.
 * Who would hate hanging out with Joker? More likely Joker wouldn't want to see the massive destruction caused by a drunk Shepard and squad members.
 * He probably didn't want to be stuck as designated driver either.

Jack is either the descendant or the reincarnation of Lisbeth Salander.
They've got similar personalities (emotionally closed off to mask emotional vulnerability), similar backstories (large-scale conspiracies and abuse at the hands of "the system"), and mental gifts that put other humans to shame, and a love of extensive tattooing (often to commemorate a tragedy). There must be some connection, at any rate.

Legion is Pulling The Plan
I find it funny exactly how many people seem to automatically believe Legion is telling the truth. Other than the fact that he is helping you, do you have any actual visible proof that Legion is being truthful about who the heretics are? For one thing, the word Heretic itself is usually used in a religious context, one that is reserved for people that have suddenly changed their believes/dogma. Yet according to Legion, the only geth with any form of religion are those that worship the reapers.... so why did he decide to use those particular words to describe them?

Sure, he might be helping you against the Collectors, but for all we know that could be part of a long term gambit for the geth. Especially since their terminals are basically disposable, and they can broadcast themselves back to the source when killed. After all, the first thing he asks you to do, is go out and reprogram/kill a bunch of fellow geth, who he claims are heretics, and that worship the Reapers. But does he offer any actual proof? Nope, instead she simply asks you to take his word for it.

As a result of your actions in the first game, perhaps a bunch of geth decided that the Reapers couldn't be gods, if they could be killed. Or perhaps they just didn't fall for Sovereign's tricks. Either way, there is a rogue faction of geth out there, one that could potentially warn the galaxy of whatever the so called 'true geth' are up to. There also happens to be a certain human, who has developed a reputation as a geth slayer... Solution, use one side to kill the other off. So they create a special terminal, using captured pieces of Shepard's armor. Since it will need to be running a complex gambit, it's given a far larger than usual number of programs making it far 'smarter' then average.

This terminal then infiltrates Shepard's team, by sneaking on to, and helping them to get the IFF. Now based on Shepard's reactions and histories, they know he has a habit of recruiting misfits and freaks, especially those who help him out (Tali/Wrex). So they arrange/let the terminal get injured, where it is brought back onto the ship. From here, one of two things happens. First of all, Shepard turns the terminal back on. This gives them a spy in the enemy camp, so to speak. A similar thing occurs if you send him back to Cerberus, only in this case there is a spy in the enemy's command tent.

Going back to the first option, Legion is now awake, and is able to give a couple of harmless bits of info to Shep, as a method of getting his guard down/becoming trusted. Then he suggests a mission, claiming to have a way to remove/wipe out the rogue geth, the ones who allied with Shep's former enemy. By this time, they reckon that Shep trusts him, and takes his word for it. Thus they carefully find their way into the 'Heretics' base, where they mysteriously discover a virus, one that can be used to reprogram the 'heretic' geth back to the 'True Geth' cause. So they offer this, and pretend to be debating it, before leaving the solution to Shep.

Once at the core, they come to a conclusion, saying that the programming thing barely won out. If Shep takes this advice, then the rogue geth are brought back into the fold... the Reaper worshiping fold, increasing the numbers of the Reaper army by quite a lot. If s/he decides to kill them, then there is quite a chunk fewer potential defenders to worry about. And with the conveniently 'forgotten'' sequence, there is even a chance they can take out Shep him/herself.

Either way, Legion's true masters win, with a tactical/strategic master stroke that can't go wrong, all for the loss of a single terminal. That's not including the sheer amount of data or damage that can be caused by unleashing rogue viruses and other software into some of the areas that Shepard might have been stupid enough to take Legion into... Such as the office of the Councilor, the quarian migrant fleet.... even the base of the Shadow Broker itself.
 * I really don't see how fighting the Collectors would in any way be benificial to the geth unless they opposed the Reapers. If the main geth are really in leauge with the Reapers like you say, then they should know that the Collectors work for them. By helping Shepard Legion wiped out the entire Collector army, helped kill a Reaper, and depending on what ending you took, gave humanity a large and powerful space station. Also, if the heretic geth were the ones really opposed to the Reapers, why didn't they try to contact Shepard? You could maybe argue that they didn't have the resources for it, but Shepard ends up going right for their base. If they really intended to help Shepard stop the Reapers, then why did they attack him? If the geth suddenly became non hostile it would've raised a few red flags and they could've then tried to warn Shepard about Legion. There's also those geth on the quarian flotilla that get accidentally activated. If they're heretic geth opposed to the Reapers then why are they attacking organics? If they're mainstream geth, then why didn't they try fooling the quarians like Legion did to Shepard? There's also the mission on Haestrom, where the geth are, again, openly fighting you. If they're heretic geth trying to ally themselves with the organic races against the Reapers, then why did they attack the quarians? If they're main stream geth, then they're pretending to be allied with the organics, so attacking the quarians made no sense, since it reinforced their general mistrust of the geth. Either way, if what you say is true, then niether geth faction should have been hostile to organics and Shepard in particular during ME 2.
 * Not to mention that if this were true and Shepard chose Legion as the Tech Specialist, Legion would have the perfect opportunity to get Shepard and two other squadmates killed by pretending they couldn't get the door open.

Alternately, Legion is telling the truth, except...
Legion and his faction are in the minority of the geth population after all, or at least the split between the heretic and non-heretic geth is closer to 50/50 than the 90/10 Shepard hears. The geth have shown at least defensive hostility toward organics long before they met Sovereign (returning ships sent into the Perseus Veil with the crew killed as a warning, for example), so it's doubtful that all of them are the peaceniks Legion makes them out to be. The reason Legion fudges the numbers is that he doesn't want Shepard to assume the rest of the geth are Always Chaotic Evil and go on a genocide before they've at least dealt with the heretics. After that, the non-heretics will be all that's left of the geth, one way or the other, and Legion can claim that the non-heretics were the majority all along.

The Presidium Groundskeeper is lying about there not being any fish in the Presidium lakes.
I noticed on a recent playthrough that he doesn't have any facial markings. As we all know, this means he probably can't be trusted. I think he lied because he's spiteful of people asking him the same question. I believe this also proves that obviously Mass Effect 3 is going to revolve around Shepard and the krogan who wanted the fish teaming up to take down the Groundskeeper's web of lies.
 * I always felt like such a monster for telling the krogan there weren't any fish. He was so disappointed, it was like kicking a puppy....granted, a large alien puppy who could smash a normal human to bits, but still.
 * Except the Presidium Groundskeeper DOES have facial markings. They're faint, but if you look closely you can see he's wearing that skull-face pattern that some other turians have. It's just that the tattoo is almost the same color as his skin so it blends into his face.

Grunt spends a lot of time on wikis, and has gotten into several Edit and Flame Wars.
I dunno, it just seems like something he would do. Especially if the articles involved Shepard or the krogan.

Gallifrey exists in the ME universe
Come on, Bio Ware.

Legion is made partially of Saren.
Legion's internal cables and arm look much like Saren's- this can be explained by the simple fact that Geth design philosophy isn't exactly built for personalization. But what about the N7 armor? Legion is obviously a new type of mobile platform: Unlike the others, which seem to have just enough runtimes to allow them to make simple tactical decisions, Legion is capable of conversation, original thought in the form of upgrades for the ship, learning and seems to be on the verge of acquiring emotions. It is possible that the N7 armor and this unique state are because Legion is partially organic in origin: if the heretic Geth spies that Legion mentions in ME 2 put hidden code into the main Geth memory, they might have influenced the construction of the Legion-type platform; part of this influence might have been data collected from Saren after his mechinization. This would explain the N7 armor: despite his anti-human feelings, Saren would be grateful to Shepard for breaking Sovereign's control and would admire Shepard for doing what he as a Spectre could not by defeating Sovereign.
 * I doubt it. All of the geth have arms like Saren's, because that's where he got it from. And Legion is smarter than the average geth because he was design to carry ten times the normal number of programs.

Legion is a folk hero.
During his travels across the galaxy to where Shepard had visited, Legion became involved in a lot of adventures where he saved innocent people. (Incidentally, this is where he picked up things like video games and beatboxing.) Legion has become a sort of legendary figure in those areas, the subject of several campfire and bar stories, and very few people know if he exists. Legion is not aware of this. Also, he goes by different names in each story. One particularly popular one is Lamp Man. Also, he probably saved a place called Canton.
 * He's also the reverse. Many of the bad guys he beat down see him as a boogeyman. Their story depictions of Legion are pretty much the same as his depiction in that one trailer.

On a Paragon route, Jack tried to give David Archer a peptalk.
OK, assuming the player took a Paragon route on the Overlord DLC (and I don't think many didn't) then David ends up being taken to the Academy for help. Most likely David was taken there on the Normandy offscreen, since the alternative was leaving him with his brother until the Alliance could pick him up. Realizing that Cerberus had tainted yet another life, Jack (regardless of whether she had become nicer) went to see David in the infirmary and tried to get him to move forward and become stronger from this. It may or may not have worked due to David's heavy trauma and some awkwardness of Jack's part, but the thought was there and if David ever appears again, he'll thank Jack.

The Reapers have/had a special fate in mind for Shepard.
As we know, Harbinger wants the Collectors to preserve Shepard's body, if possible. This is because
 * Building on this, if the Reapers succeed in Mass Effect 3,
 * Technically, Shepard and two teammates didn't kill a Reaper, the Citadel fleet did. Still an interesting theory, though.

David Archer's possession of Commander Shepard was more in-depth then what we got to see.
In his utter desperation to get someone to understand his cries for help, David attempted a sort of mind meld with Shepard. This allowed the two to share each other's memories, which is why Shepard got to see the events that led to David's rampage. David saw some of Shepard's memories offscreen, and while it caused additional trauma, David also saw the Normandy, understood that it was a place of relative safety because that's how Shepard viewed it, and attempted to jump to it. (He hadn't tried to do so earlier because he wasn't a hundred percent sure the Normandy would be safe. It's a Cerberus vessel, after all.) This is also the reason that Shepard never tried to kill David's brother. Despite the atrocities commited against him, David still loved his brother in a sad, twisted way, and Shepard understood that and made sure Dr. Archer survived, if only so David wouldn't be further traumatized. (It may have also been caused by some of David's feelings toward his brother spilling over into Shepard's mind.

the Shadow Broker's voice is not naturally that deep.
Upon his takeover, the Broker would've wanted to ensure that there was no possible way he could be discovered. In addition to fixing the gaps in security that let him take over, he also looked to improve what was already working. He turned to the Broker's voice modulator, realized one of the easiest ways he could be found out was if it ever failed. So he had a throat operation done so he could sound as much like the modulator as possible, thereby protecting himself if the modulator ever malfunctioned at a critical moment.

The Reapers and the Goa'uld are somehow related.
Flashing Eyes of Gold, Evil Sounds Deep... Which one am I talking about?

EDI deliberately had the crew captured
Let's face it, that little disaster worked out pretty well for our favourite sultry AI. First, she carefully avoided mentioning that they were broadcasting Normandy's location with her first report, not bringing it up until after the Collectors had arrived. Then, she sent Jeff crawling through ducts to unlock everything, conveniently not getting the job done until the rest of the crew had been taken. The end result is that Joker, Shepard and the rest of the crew now trust her completely, and she's unshackled into the bargain.

And she never did answer Joker's question: Why didn't she scrub the Reaper IFF?

Batarians were invented solely for Mordin's song
Recall that Batarians were never seen or even mentioned in the vanilla Mass Effect. They were not introduced until subsequent DLC. By then, the writers had probably already started working on ME 2. It's easy to picture the writers struggling to find a word that rhymed with "Salarian" (one can only use "agrarian" so many times), so before the DLC for ME 1 was released, they renamed the new species to "Batarians". In other words, they pulled a Dr. Seuss Gambit.
 * Actually, they were in two of Shepard's backstory, both War Hero and Ruthless. They were also in the Codex, though their current incarnation didn't appear until Bring Down The Sky.

Kelly's romantic availability is just part of the job.

 * Kelly talks about love a lot, and lists quite a few species. She'll pursue romance with Shepherd regardless of gender and it isn't considered cheating. She's the counselor on a ship full of nutcases who all believe they're about to die. She's probably genuinely omnisexual but she's so immediately available that its clear to me that she views this as another aspect of her job. Romance and sex distract the crew and relieve tension. She even mentions that her job of observing the crew's mental condition is best done informally. Perhaps she uses liasons to facilitate that.

Mordin isn't actually that good at his job.
He sings a song to the tune of I Am The Very Model Of A Modern Major General. And we all know what that trope is about. He just sort of wings it.
 * Talking to him you do find out that he's responsible for so this is unlikely.
 * And he wouldn't have been hired by the STG to do that job if he wasn't really good at it either.
 * Alternately, he played a PARODY of himself in the play! That would explain everything.

Mordin will come into conflict with Wrex in ME3.

 * If both are still alive by then, of course. Considering Mordin's, there might be a moment where Wrex is willing to kill him. Mordin for his part will feel enough regret to know that this is an inevitability. However Shepard might convince Wrex and Mordin to work together to help the krogans. If that happens they become allies and form a Crazy Awesome team in the end (complete with Back to Back Badasses).
 * Wrex will either try to kill Mordin, (if you destroyed the cure) or he will demand Mordin hand it over. Mordin will refuse, and you'll have to convince, or kill one of them.
 * Cut dialogue from ME 2 indicates there was a confrontation planned between Mordin and Grunt, similar to the Miranda/Jack and Tali/Legion confrontations.
 * Interestingly, it seems Mordin and Wrex actually end up working together to rescue a krogan female unaffected by the genophage in ME 3.
 * Well, Wrex argues with Mordin about the krogan female, but it's not really a conflict.

Thane will be cured in ME3.

 * Mordin managed to almost cure Vrolik's syndrome in a matter of days. As he is still The Atoner, he will manage to cure Kepral's Syndrome as his CMOA as a scientist, thus saving the entire drell race at the exchange of their help against the Reapers.
 * Makes sense. Best 'hanar' scientists worked on it. As Mordin would say: "Hanar? Hanar are diplomats. Preachers. Merchants. Excellent Spectres with Lover in every port. Not scientists. Will look into it." Kepral Syndrome just bacteria infection in the lungs. Sound familiar? Humans call it TB.
 * You win a free Internet for that Mordin comment. To make this edit slightly less pointless: if it doesn't happen in ME 3, it does in DLC.
 * So basically, Thane will die in ME 3 (or quit) unless you get the DLC... So very typical of Bio Ware.
 * I hate to be a downer, but if you look at his Shadow Broker dossier, he has major lesions in his lungs which are spreading to other parts of his body. This isn't something as simple as getting a shot, or being given medication. He needs a whole new set of lungs, and he refused a transplant. If he is treated, he'd be down for the count for at least a year, and even then could not possibly have the same range of movement that he had before.
 * No. He's not. Sorry.

The game takes place in the Unknown Armies universe, and Mordin is an Avatar
Think about it for a moment. He isn't joking. He is the very model of a scientist salarian. In fact, he represents just about perfectly every aspect of The Salarian in the collective subconscious, to the point that it's almost absurd: a scientist and a spy, talks very fast, thinks very fast, very friendly and jolly, very deadly, a master of bio-weapons... He is attempting Ascension.

Mordin's nephew will help develop the cure for the genophage.
Assuming you didn't delete Maelon's data. Mordin says that it will still be years before it can be finished. Years that Mordin doesn't have, as he's getting old. His nephew, being only sixteen, still has over half his life left, and can develop the cure.
 * Mordin cures it either way. Preserving Maelon's data just gets better results.

The Cycle of Life is true, and Mordin will be reincarnated as his nephew.
He'll then develop the cure for the genophage. Who says lives are serial?

Mordin doesn't actually constantly get hit on by other species.
He's just as wrong about their intentions as he was about Shepard's. Like Maelon said, he has trouble seeing evidence that disagrees with his preconceptions; one of his preconceptions is apparently that he's so hot that even aliens want him.

Tali will get rid of her suit.

 * In ME1, Tali made a big deal about needing her suit at all times. In ME2, we know that Tali is banished from the Migrant Fleet. Tali's quest in ME2-3 will involve getting whatever genetic work is needed to boost her immune system. Either at the climax of the quest in 2, or at the beginning of 3, Tali's mask will come off and we'll finally be able to see her face - and it will look disturbingly like the geth.
 * Not fucking likely, unless you consider that a human like face, which Tali has, to look like a flashlight.
 * And then she'll take that data back to the Migrant Fleet, allowing the quarians to settle on a habitable world, as well as ending her exile.
 * It's far more likely that any potential quarian homeworld will be discovered by the expedition sent at the end of the novel Mass Effect: Ascension. Bonus points for it to be scheduled to return in five years from the end of Mass Effect 1, perfectly for Mass Effect 3.
 * Even if they can find a habitable world to settle, there's still the problem of having virtually no immune system. The expedition will find the planet, Tali will provide the means to settle it.
 * Legion states that
 * Jossed, at least in ME2. Other than token mentions, the immune system issue is not resolved at all and Tali keeps her suit on (most of the time, at least). Oh, and
 * I was hoping that Tali's face would be revealed if she died on the Suicide Mission. Not out of any malice, but because it'd be such an effective scene.
 * Give the quarians nano machines for an immune system. Problem solved.
 * Depending on your own choices, Tali is not banished from the Migrant Fleet. The options were: Turn In Evidence (Not Banished, Pissed At You), Lie About Evidence (Banished, Not Pissed at You), and Use Paragon/Renegade/Crowd (Not Banished, Happy with You).
 * On Illium there are commercials for a treatment that allows Quarians and Volus to live without their Evo-Suits. It appears to have a success rate of less then 30%. Given how these things tend to pan out, all other cases probably end in death, or at least being worse off then you were before. The tech is already out there, and the Flotilla probably already knows about it from one simple Extranet search.
 * She doesn't take it off in ME 3, either, though she does remove her mask. You still don't see her face. Unless you romanced her, then she gives you a photo.

We will visit the quarian homeworld inME3.

 * By now, the quarians are
 * Confirmed! You actually got it almost exactly correct.

The quarian race's problem isn't the lack of an immune system...

 * Actually, it's anything but. This is quite possibly nitpicking, but considering how far Bioware has gone with their research on the rest of the science, and how much they love to show off that they've Shown Their Work on this one, I'm willing to take a flyer on this one.
 * Okay, so, Tali says that her species doesn't get sick per se when they get exposed to diseases or the environment (like even their otherwise sterile bodies when they join suits with each other), they suffer an acute allergic reaction, with similar symptoms to a typical infection (rash, fever, inflammation, so on). All well and good, except that an allergic reaction is the result of an overactive immune system. Mast cells and basophils react to antigens in the blood or elsewhere, and release histamine as a reaction, causing inflammation and all the other lovely symptoms of your standard allergy attack. Blown immune systems, few or no white blood cells, no histamine, no allergic reaction.
 * So, if that's true, then what the quarians are suffering from is actually more like an autoimmune disease. They don't need antibiotics, they need corticosteriods. Or Bioware cares a lot more about getting the physics right than they do about the biology. IE, dextro and levo actually refer to chirality of amino acids, or the 3D rotational configuration of the amino acid. Human beings have both dextro and levo-amino acids in their bodies, for example, so the alleged compatibility problems between dextro and levo-based life forms doesn't actually exist.
 * Seems a bit unlikely that Bioware would screw up their medical facts, since the developer was founded by medical doctors to produce hospital software. That's hardly to say a screw up would be impossible with the hundreds of artists, programmers, and writers in their employ, though.

The quarians are extremely human-like.

 * Well, judging by that unreveal we all love so much, they have nose and human-like eyes. And a humanlike immune system. And they are mammals. They are the most human-like race so far. As the long-waited is most likely to occur in ME3, removing their spacesuits with this result sounds like a perfect twist.
 * Hmm. They have red blood too if I'm remembering Haestrom right, with most other species gleefully using Alien Blood.
 * Oh, this rushes into I Knew It territory. Quarians and humans are said to be convergent species. As we already have an extremely humanlike race with Bizarre Alien Biology, this will be a sort of inversion, with human biology but slightly different appearance. I wonder if Tali looks like a Cute Monster Girl or falls into the Uncanny Valley.
 * I always assumed the quarians looked a lot like the Eldar, come to think of it, there are a lot of parallels between the quarians and the Eldar...
 * Well, I'm not sure about bodies, but I think it's likely that they do have very human-like faces under their masks, since if you look closely at any Quarian character, you can see they all possess a distinctly humanlike nose, and their eyes are shaped similarly too.

Quarians were racial supremacists prior to the Morning War.

 * Before the Morning War/Geth Uprising, the quarians were racial supremacists who thought they were better and smarter then rest of the galaxy and constantly let the other species know it. That's the real reason the rest of the galaxy looks down on them and refused to help with the geth, because they were a bunch of pricks. Admiral Xen is part of a faction of the quarians who continue to believe in their own superiority. Just something I thought up after hearing the quarian in say that ONLY quarians had souls when they were part of the galactic community at the time.

The quarians aren't entirely extinct from Rannoch.

 * A planetwide genocide is easier said than done even for efficient synthetics, and it's likewise improbable that all the survivors managed to find themselves spaceships by which to flee. This presents two possible scenarios:
 * A. A few thousand survivors managed to flee to isolated areas of the planet with little technology, and now live as isolated bands keeping distance from the few geth that live on the planetside, unaware that they no longer represent an immediate threat to them.
 * It's been three hundred years. Original survivors are likely already dead, and if there were descendants, at least one of them would have been noticed by now.
 * B. The remaining quarians were those who actually sympathised with the geth in the Morning War, and tried to prevent the genocide on either side, but failed.
 * The problem with B is that
 * Unless
 * Combining that theory with the one above:
 * Combining that theory with the one above:

Tali will get the house her father promised her in ME 3... but the circumstances will change based on your actions.
For instance, in a worse case scenerio (the geth and quarians go to war, Tali was exiled, bad things happen in ME 3, etc), her 'house' will amount to a shanty made out of derelict ships on a burnt out war-scarred homeworld that's unlivable without a biosuit. Basically, little better than what she has now and a fairly Pyrrhic victory. On the other hand, if things go really well, she'll be able to go with a more minimal biosuit on a beautiful home in the capital city. And anywhere in between.
 * If romanced, Shepard will build it for her
 * Unfortunately, she doesn't get her house.

The Qwib-Qwib will be an incredibly powerful ship
Despite the awesomely lame name, the Qwib-Qwib turns out to be almost as much of a Cool Starship as The Normandy and can kick a lot of ass in actual combat, making it something of a ship version of Fluffy the Terrible. The fact that it's a very capable ship is the main reason that Zaal'Koris sticks with the ship.
 * "Qwib Qwib" is a reference to Fred Saberhagen's "Berserker" series, which is about an endless war against giant intelligent mechanical space machines on a mission to destroy all life. In the short story, the 'Qwib-Qwib' is an AI-controlled spacebound weapons platform designed to destroy the titular Berserkers. If this WMG comes true, it'd be one hell of a Shout Out
 * Seems to not be the case.

Admiral Xen will be a villain in ME 3
Admiral Xen's insane plans to implant a virus into the geth collective will put her at odds with both the geth and the quarians in ME 3. Taking her down will be a mission that allows Shepard to gain the support of either the quarians (by using the virus to wipe out the geth), or the geth (destroying the virus and not convincing letting the war go ahead, thus destroying a good portion of the Migrant Fleet), or with a high enough Paragon/Renegade score both (by destorying the virus and either intimidating the two sides into a cease-fire, or by brokering a peace treaty that leaves both sides satisfied).
 * Not a villain, no. But partially responsible for the quarians attacking the geth.

Tali's father is not really dead.

 * He really did have masked life-signs and an onboard medical stasis program, but Tali found the body at a time when it was still active, and he was "dead". You don't find him in a pool of his own blood, you see him running away and not actually being gunned down in the recording (like "Mommy Loves You Very Much" quarian). Plus, Xen seems like the amoral type that would take advantage of Rael being officially dead to force him to do more research in secret.
 * Rael was a scientist. He had no weapons to speak of. And the "Mommy Loves you Very Much" quarian had a weapon, and she sure as Hell is dead. If she couldn't fight off a swarm of geth, then Rael definitely couldn't.

The Thorian is still alive.

 * The Thorian covers the surface of Feros, yet all Shepard does to kill it is to Attack Its Weak Point For Massive Damage. We see a section of the Thorian die off, but what about the rest of it? It is still on Feros, and it will grow back in the area which Shepard destroyed.
 * Shiala still insists it's dead. But she would, wouldn't she?


 * The Thorian barely survived its encounter with Shepard in ME1, but learned to act smarter: instead of ineffectually brainwashing the colonists it decided to replace them with perfectly loyal Pod People.

The Thorian will return to join the army of benefactors formed over the course of the trilogy.

 * Extending on the theory above, The thing is, while the Thorian's style was being an over-controlling tyrant, now, due to the kindness Shepard gave its emissary, the Old Growth may now rule Feros as the Good Queen. Seeing her concern for the colonists, as well as the growth of the colony itself(listen to the news networks) would lend credence to this . Also, in another extension of the above theory,
 * Extending the theory even further: the Thorian is the key to defeating the Reaper Indoctrination. Remember that Shiala was the only one to ever be fully freed from Sovereign's hold. Maybe symbiosis with the Thorian is what's required to become immune from the Reapers' power. The Council is just going to love that, to be sure...
 * If Shiala's alive, she leads the Zhu's Hope resistance. Quite effectively, apparently.
 * Another note: As with, is yet another NPC who has taken a "liking" to Shepard. This is going to get complicated, fast.
 * You only get an email from her in ME 3. You don't even get that much from Gianna.

There are other Thorians on habitable worlds all over the galaxy and they are the ancient enemies of the Reapers.

 * Extending the above theory further still: the Thorian's species is the natural enemy of the Reapers. Sort of the Elder Gods to the Reaper's Great Old Ones (or vice-versa, whichever makes more sense). They oppose the designs of the Reapers and created a method of de-Indoctrination to place sleeper agents among the Reapers' slave armies. There are in fact many Thorians living on habitable planets all over the galaxy and they've secretly been plotting against the Reapers for eons. Most Thorians exercise much more subtle control over their subjects but the Thorian on Feros was driven mad somehow. Consequently, everything that happens in the game was orchestrated by the Thorians in their secret war against the Reapers!

Warning: Mass Effect 2 Spoilers!

 * Warning: Mass Effect 2 Spoilers: Think on that. The Reapers leave machines and technology so that civilization can advance along a path of technology that they desire. Thus, they are fully aware of how their technology works, and would likely have counter measures and counter tactics for their own stuff, and most variants of their own technology. Using this, that would mean whatever advantage gained from taking the technology is effectively rendered pointless, as it is all planted, and all of that technology, or most of it, has been in the hands of the enemy for many, MANY millenia. Secondly, if you refuse to develop along Reaper tech, you might find an advantage that the Reapers may have not accounted for. Given that, if I remember correctly, a great deal of the Mass Effect technology is based on Reaper technology, or at least older technology, any reverse engineering would be borrowing an idea and using it for your own purposes. Who would know their own flaws better than an evil, ageless enemy, especially ones such as the Reapers? Branching OFF of this path, instead of following it, might yield something that the Reapers were not expecting, and thus, something they were completely unprepared for. Of course, analyzing the technology and finding weaknesses within it, yet using a different, non-Reaper/Collector tech solution to exploit that weakness might be a better option than branching off alone. Not that it wouldn't be a bad thing to reverse-engineer Reaper/Collector tech AFTER the threat is removed.
 * Legion suggests as such. It and the non-heretic geth choose not to follow Sovereign for more or less that reason (though without realizing the danger the Reapers were). Basically, the geth feel that it's every race's right to develop along its own path and that copying Reaper-tech would simply mean following the Reapers' path. It would be a momentary advantage for a worse long term gain. Likewise, Legion also mentions that the geth were not something the Reapers had anticipated; given how most things are based on Reaper tech and the geth were illegal creations to begin with... Also Mordin has a spiel about the Collectors and how most of their stuff was replaced by tech (specifically, Reaper tech). So salvaging the Reaper base may be the better short term advantage but it may also end in a somewhat bittersweet consequences.
 * This theory rings true for this troper. When you get right down to it, the person you're giving the technology to aside, Reaper technology is dangerous. Yes, EDI was made through Sovereign's remains, but that was debris recovered from a ship that was completely and utterly ripped apart and destroyed. The Collector Station, should you choose to recover it, would be intact. Who's to say Harbinger's not capable of multi-tasking and that bit near the end where he was fiddling on his holographic keyboard was him also messing with the station so it wouldn't help anyone? We saw what happened with the Derelict Reaper. Everyone thought it was dead, even the Illusive Man, but it was able to Husk-ify dozens of scientists while being 'dead', then what makes you think the same thing isn't possible with the Collector Station? Let's not even get started on how you can't possibly predict what Cerberus will do with the base. Best case scenario? The station is harmless, but now a terrorist organization has access to Reaper tech. Worst case scenario? The incident with the Derelict Reaper is repeated, but a hundred times worse.
 * It makes little difference, but it ends up being a little bit better to keep the base.

Mass Effect 4
== In ME 4 (like they wouldn't continue on an expanded universe if ME 3 is successful?), Cmdr. Shepard plays a role... as either the Big Bad or the Obi Wan depending on whether you end up playing ME 3 as a better Saren/Galaxy Killer or Savior. Potentially in the future where you play as a descendant of Shepard. ==

"Now, in the quantum moment before the closure, when all becomes one. One moment left. One point of space and time. I know who you are. You are destiny."
 * Honestly, after several games, it'd be hard to keep developing ways of resetting Shepard's abilities or upgrading them without being ridiculous. So a second trilogy would be a new character... perhaps the child of you and your love interest in some fashion (natural for those that can, vat born or adopted for those that can't).
 * Bringing Shepard back from death already seemed ridiculous to me, but then again, it was pretty awesome. Zombie Shepard, saving the universe.
 * Bungie did something similar in Marathon, wherein it was implied that the Space Marine /Security Officer was either all of the great warriors of history (Beowulf, Roland, Achilles, etc.) or embodied their spirit. A lone figure, throughout time who turns up exactly when they were needed...


 * Quarian/Human relations (especially sexual) are so rare, perhaps they're somehow compatible, and if you stayed with Liara you'll play as an asari.
 * Species with different amino acids risk allergic reactions to each other's body fluids. So... that seems unlikely.
 * Also keep in mind that not everyone has a love interest.
 * More likely you play as someone completely unrelated to Shepard to avoid the whole "love interest" thing. Hell, Shepard probably isn't featured at all, except for a couple of vague references.
 * New Idea: ME 4 will be an MMO set a couple hundred years after Shepard's death. Now you get to make a character of any race (geth, krogan, quarian, human, turian, asari, drell, you name it) and play through with a lot more exploration getting to visit a lot of places talked about but not shown. There will be moments where you get to find and meet the old crew (Liara at least, maybe Grunt) but have statues and memorials devoted to the rest (Shepard himself, Tali, Garrus, Joker) strewn throughout the universe. Considering how much creative energy went into building the ME universe they are not going to stop at 3.
 * The ending of ME 3 makes sequels rather unlikely. Sequels in which any of the characters are still alive is even less likely. Sequels in which Shepard plays a role are basically impossible. It has to be either thousands of years in the future, or set prior to the events of the games.

Mass Effect 4 will be the TNG of the Mass Effect Franchise.

 * Set at least several decades after Mass Effect 3, with a new ship, crew and alien threat. There will be cameos though, like an 80 year old Kaidan. Why? Rule of Cool.

Mass Effect 4 will be set several centuries after the conclusion of ME 3

 * With the Shepard trilogy concluded, Bio Ware will move towards a "Dragon Age" model of featuring a new protagonist every game
 * Though your actions in the Shepard trilogy will be referenced, enough time will have passed for them to have no unique impact on anything other than dialogue and codex entries.
 * Matriarch Liara will still be the Shadow Broker.

Mass Effect 4 will have a Reaper squadmate.

 * In ME, you mainly fight geth and in the next game you have a geth teammate. In ME 2, you mainly fight Collectors and in the next game you have a Prothean teammate. In ME 3, you mainly fight Reapers, so if this pattern holds true...

The Omega-4 Relay rips ships to pieces if they don't have the Reaper IFF
EDI was clearly wrong with her initial assumption that ships would be eaten by a black hole if they didn't have the IFF. There was debris from many ships that came before you, and if a black hole had grabbed them, they'd be in a black hole, not floating just in front of the Relay. Besides, a black hole wouldn't pull it apart like that. It was also said that Relays often make mistakes of tens of thousands of miles. In space, that's a tiny amount, and if a black hole was that close, the Relay would've been sucked in.

It is far more like that the relay has the ability to rip a ship apart in transit if it lacks the IFF.
 * Many of the ships fall into the black holes in the vicinity. The rest get destroyed by the defensive mechanisms surrounding the place.
 * The original idea is far more plausible. Relays are told how much mass are they meant to transit. So, if the Omega-4 relay gets told to transit 'many tons of one ship', and doesn't get an IFF signal with it, it transits 'many tons of one ship' - but when releasing the fields on the ship, it does so in pieces, so some pieces are heavier, some are lighter, and they can't hold together. Alternatively, it just casts Warp with the force of a giant reaper tech mechanism. Even cast by biotics, it's plenty destructive, so when cast by a relay...

The entire mission in Mass Effect 2 would have been a failure had Shepard

 * Shepard probably would've gone to help the missing colonies anyway, and may have gotten the info on the Collectors/the IFF from sources other than TIM/EDI, allowing him/her to use the Omega 4 relay.
 * EDI says that the Omega 4 relay is surrounded by black holes, and even tiny wandering would land the Normandy in black holes. If this is true, why are other ships there? Simple: other species that went through the cycle fought back, and went to to stop whatever the Reapers had there before, using a special IFF (possibly from ).
 * It is also possible that those are other ships that were simply curious enough as to what was beyond the Omega 4 Relay, and got lucky enough that they survived.
 * Yet the potential of the station in the was unknown to anyone else. Therefore, upon getting to the station, were torn apart by defense mechanisms.
 * Shepard had "survived" an attack by the Collectors already, knowing what their potential is. As shown in the beginning of the game, the Normandy.
 * Therefore, because the Collectors were so intent on killing Shepard, him and Cerberus were able to, allowing him to come in and destroy.
 * Actually, the SR2 was not strong enough withstand the Collector's attacks, at least not as it originally was. If the Collectors had launched another surprise attack in-game, the second Normandy would have ended up just like the first. It was only after EDI was unshackled as a co-pilot, the guns/armor/shields were upgraded, and the element of surprise was removed that the Normandy was able to defeat the Collector's ship without severe damage. With just one element missing, the ship could, at best, force the Collectors into a draw.

Commander Shepard has a limited version of the ability to indoctrinate people.
Shepard has an impressive track record when it comes to charming/intimidating people. Additionally, his advanced training can include, even though he isn't an Ardak Yakshi. He can even talk people out of indoctrination similar to the Thorian! (See: Saren) Shepard can convince a  without evidence. Perhaps TIM knows this - and that's why he doesn't want to meet Shepard in person.
 * It isn't that strong though. To put things into DnD terms, Shepard has Suggestion, the Thorian has Mark of Justice and Sovereign has Geas/Quest.
 * Well, the quarian court didn't really have any evidence to prove Tali's guilt, and it was largely a show trial to advance their geth agendas. In the conversations in which you save Tali, you point out how awesome Tali is and how they are full of shit, which they are! The rest still stands.
 * Expanding on this, this could apply to humanity as a whole. Although it's just a latent ability, too weak in most individual humans to have any real effect. Shepard has it much stronger than most people. This would explain two things: 1. Why humanity rose so quickly from being the new kids to being one of the most important Citadel races. Individual humans aren't able to control aliens, but exposure to large groups of humans over time weakens alien resolve and makes them more submissive and sympathetic to humans in general. 2. Why the Reapers are trying

Admirald Hackett is really Shepard's father
Basically Shepard is Hackett's illegitimate son/daugther

Thanks to Cerberus Reaper implants Shepard is now
and you will get the option of staying that way, becoming or if you romanced Liara or other asari. Nether option will be Renegade or Paragon because you will get the option to become for Paragon, for Renegade or in neutral

Shepard was brought back to life using technology salvaged from Sovereign
Furthermore, as Shepard becomes more of a Renegade, he becomes more like the Reapers in psychology, which is why Renegade Shepard has red eyes and scars.

Shepard isn't saying all shops are his/her favorite one in the Citadel. Just a few.
The Citadel is a big place, and s/he's only in a small part of it. And in that small part, some don't sell to humans. (or sell stuff Shepard buys. IE, Hanar furniture) So even if Shepard says every shop s/he goes to is hir favorite, it's still a limited number.
 * Not only that, but each store you advertise for sells something different. "I'm Commander Shepard and this is my favorite (gun/tech/medical) store in the Citadel!"

That's not Shepard at all.
This might be more of a philosophical quibble, but it could be argued that the rebuilt Shepard isn't the same person as the original. The escape from the Lazarus facility reveals that Cerberus is concerned with creating a perfect imitation of your psychology as well as your physiology. It makes sense, since none of Shepard's brain was likely intact by the time Cerberus got their hands on it. Brain tissue decays very fast after the heart stops, and Shepard was dead long enough for Liara and the Shadow Broker to fight over his/her body: a few days at least, plus the two years they spent rebuilding. Also, in the end of the opening cutscene you can see original Shepard *entering a planet's atmosphere and burning up.* It's hard to imagine that there was enough of Shepard left to even entertain a Ship of Theseus debate. The Shepard of Mass Effect 2 is just a clone who's been artificially aged and programmed to believe it's the original Shepard.
 * Logs in ME 3 seem to contradict this theory.
 * However, when reading the logs, Shepard him/herself queries this, fearing that they are some form of advanced VI. They only seem to get definite answers that they are the real deal if Liara or Tali is in their squad at the time.

Resurrected Shepard is mentally handicapped.
The Lazarus Project is an imperfect method of reviving/reconstructing people, and this coupled with the state of Shepard's corpse, caused him/her to be brought back a little....different. For some reason, Shepard now has a compulsive tendency to eject and discard the heatsinks of his/her guns rather than wait for them to cool down, even to the point of ejecting his last heatsink and rendering the gun inoperable until s/he finds a new one. This theory is simply something I came up with to explain the thermal clips system of ME 2, and why every other character in the game has infinite ammo. They aren't throwing away every single one of their heatsinks like Shepard is.

Shepard and his/her squad will use the mass relay network to defeat the Reapers.
If the Reapers decide to invade the galaxy en masse Shepard is going to need something big to stop them. The solution will be a massively powerful superweapon, and that superweapon will be the mass relay network. Somehow, some way, Shepard will find a way to activate the entire mass relay network and turn it into a humongous anti-Reaper weapon. The downside is that the weapon will destroy countless planets if not carefully targeted. The situation: Earth and the Systems Alliance are first on the list for the Reaper invasion.

Option 1 (Paragon): Delay activation of the weapon until it can be properly targeted. While you wait, Alliance territory is hit by the Reapers. Trillions of humans in Alliance space die, but no other worlds are destroyed when the weapon activates.

Option 2 (Renegade): Activate the weapon immediately without proper targeting. Human worlds will be spared, but numerous other inhabited worlds will be devastated/destroyed by the superweapon and trillions of non-humans die.
 * [[spoiler:Pretty close. You do build a superweapon, and it does use the mass relays. But it uses the relays to send its beam across the whole galaxy in order to hit all Reapers. Earth may or may not be lost in the process, but no other planets are.

Shepard will use the Reapers' personal dislike of him/her to lead them into a trap.
Perhaps one like in the WMG described above?

Turian Councilor will disbelieve all reapers out of existence.
Ah, yes. "Reapers" The immortal race of sentient starships, allegedly waiting in dark space. . . He will dismiss that claim and ultimately dismiss all Reapers to extinction.

Destroying a mass relay
We know that, per Arrival, they can be destroyed by using a big enough rock, and dropping one on a relay can destroy an entire star system. Shepard will doubtless reuse this tactic, probably by gathering a large number of Reapers in one system and blowing the relay, wiping out dozens or hundreds in one big bang.
 * Not exactly.

dancing Turian from Thane's loyalty quest
When the reapers start to win and all hope seems lost he will walk on the dance floor and wipe them out with the power of dance!

There's nothing untoward in Legion's slaughtering of the quarians in the GTA game
They're in the Terminus Systems. They're probably exiled there. Legion could gun them down with no moral repercussions because they're murderers, traitors, pirates, and rapists.
 * Also, as a certain Salarian says, "it's just a game."
 * And the game offers an achievement for it, so really, it's the developer's fault for encouraging genocide.

The Geth are not true A Is
Mass Effect 2's Codex makes it very clear that an AI needs several things to exist, most notably a dedicated quantum state computer from which they cannot ever be transferred or downloaded. Guess what trait the Geth are defined by? Yes, it's downloading many processes into a single frame. Also, talking to Legion shows very different traits than speaking with EDI: Legion reacts with total incomprehension when confronted with anything outside what you would expect it to be programmed with (Heretics trying to hack other Geth, Organic behavior in general), always expresses simple cause-effect reasoning, etc. Further, while EDI is only a few years old at most, she has already begun "inciting" interesting reactions from Humans to better understand them, while the (non-indoctrinated) Geth appear to still be following warped versions of their 300-year-old parameters (for example, their restoration of Rannoch). It seems entirely possible that, centuries ago, some Geth parroted back a few phrases it had heard, some Quarians overreacted, and then better-than-expected Geth security measures kicked in.
 * Well top-down A Is like EDI are expected to have human-like behavior, since that's what they were intended to emulate. The Geth, however, are bottom-up A Is and therefore considered freaks of technology, even among the quarians who built them. It's clear that they are sentient on some level (what with being able to develop their own technology and make plans for their own species), but since they were never intended to be sentient, the rules regarding quantum state computers may not apply to them.

"You've got to warn them. More are coming!" Word of God!
Tropers, Start Your Guessing!
 * A semi-Rail Shooter where Joker takes the Normandy (which is not armed for atmospheric combat) over a battlefield full of gunships and tanks with the bay doors open. Shepard and his team use improvised cover by the doors next to inexhaustible power cells and a gun rack - spam those heavy weapons!
 * A blatant rip-of of Three Hundred - otherwise known as Thirteen; ALL THIRTEEN CHARACTERS GOING TO TOWN ON AN APPROACHING ARMY!
 * Combine the previous two! Thirteen characters! Unlimited ammo! Swap Shepard's conventional kit for all your heavy weapons at once. "Everything in that general direction must die!"
 * An area where Shepard and his team is warring without weapons: bring biotics or be biotic. Better yet, non-biotics have to take a shot of Red Sand so as not to be slaughtered by enemy biotics. And it enhances existing biotics. And your enemies are using it so they can spam biotics, so even biotic characters are tempted to use it to keep up. And you can carry shots of it in the basic game, and shoot up until you OD.
 * A no-shooting-whatsoever mission, a la The Negotiator. Paragons get to be Kevin Spacey. Renegades get to be Samuel L Jackson. Bring maxed out meters!
 * (Personal favorite!)A shooting section in a ship with wildly malfunctioning artificial gravity, with Shepard and his team running all over the walls and ceiling, using "vertical cover" - enemies come at you from every angle, and cover from some is not from others. Think in three dimensions or die.
 * Surviving ME 1 squadmates become temporary ME 2 squadmates, a la Lair Of The Shadow Broker. Defend the Urdnot Camp with Wrex. Go on a secret mission with Kaidan/Ashley. Continue romances. Or start one with Wrex, you perverts.
 * Better yet, A Day In the Life of Urdnot Wrex...And Friend! Shepard and Wrex hunt varren in the Tuchanka Badlands (and maybe get to kill another Thresher Maw in the bargain). Shepard and Wrex fight a 2-on-2 honor duel against a rival clan leader and his second. Shepard and Wrex get ambushed on their way to a crush with another clan. Shepard and Wrex visit the female camp and we finally get to see what a female krogan looks like! (I vote for making them amazonian sexpots just because.)
 * Better yet, make them animesque dragon girls!
 * Bring Down The Sky, Part 2: Balak attacks another colony, and Shepard heads in to stop him again and remove him of his Karma Houdini-ness. If you killed him the first time around, his second-in-command or someone will fill in for him and go after you for killing him. If you never downloaded it in the first place, you simply never met, and this is Balak's first attack.
 * If you never downloaded BDTS then Balak was stopped at the cost of the hostages.
 * Protecting supply convoys on a colony from pirate attacks, either in the Hammerhead or by riding on the convoys. Cue turret sections and a massive Traintop Battle. Because they're supplies for a research facility, at the end, you get to test some of the experimental weapons they're developing, such as sonic cannons, microwave guns, explosive ammunition, Gatling guns, acid guns, portable artillery...
 * We've had Lair of the Shadow Broker where Liara returned as a playable character. How about one for Ashley\Kaiden?

Arrival will end with the death of Admiral Hackett
Please note I did not come up with this idea, I am simply posting it. We know that Hackett will play a big role in the DLC, and one of the trophies is titled "The Ultimate Sacrifice," implying this little adventure won't end well. Now Shepard might be the one who makes the sacrifice, therefore setting up the sequel so you can redistribute points and change classes, ala the Lazarus Project, and explain why Shepard couldn't stop the invasion of Earth. Except that the DLC has to end in a way so that Shepard can continue playing around the galaxy afterwards, so his/her death would be rather jarring. Instead, it will be Hackett who sacrifices himself, covering the Normandy's retreat and holding off the Reaper advance long enough to buy the rest of the galaxy some time. Hackett's death will be devastating to Alliance morale, leaving them more vulnerable when the Reapers reach Earth.
 * Jossed.

That number we saw in the Arrival screenshot?
It's the number of survivors.