Aethyta threatens to use a singularity on unruly customers, in ME 3 we find out she is Liara's Farther, Liara is the only other character apart from Shepard who uses singularity.
You bust Jack out of Purgatory, a prison ship held by the Blue Suns. Now, the merc gang they belong to might not matter, but think for a moment. The Blue Sun(s) hold a girl who's badass, a trained killer, and insane. If this is starting to sound familiar, she can kill you with her brain. They used them for yet another Firefly Shout-Out (the Blue Sun Corporation are the jackasses who were a large part of the Academy's funding/control). Someone at BioWare must really like Firefly. That same Firefly fan/BioWare employee must also like Riddick if he'd name a badass bald chick 'Jack' (a badass bald chick named Jack who is rescued from a maximum security prison).
The mechanic from Horizon in ME2 blames Shepard and the Alliance for bringing the Reapers down on the colony, despite the fact that other neutral colonies are being targeted and the Alliance defenses used by Shepard are exactly why most of the colony was saved. Yes, he's a coward for not helping out... but Shepard and the Illusive both agree that it is too big a coincidence that the Collectors target a colony where one of Shepard's crew is stationed, so technically he was right.
The principal villains of the game are the Collectors. You could buy a limited Collector's Edition, whereupon you got The Collector's armor as a bonus. It's not an edition for collectors. It's the edition OF The Collectors.
Jack's character design seems too over the top at first. However, it is common for abuse survivors to get tattoos and piercings as a way to reassert control over their own body.
Coming back from the dead, the title "Spectre" suddenly fits Shepard so well.
If you buy an upgrade from a store, you don't need to research it, unlike all other upgrades. Why? Well, stores would rapidly go out of business if the buyer had to build it themselves; you're buying the full, researched, completely built product.
One of the first things you behold upon entering Omega is a line of people queued in front of an elcor doorman. Elcor are pretty perfect for the role: They're polite, reasonably perceptive, armored far beyond the ability of some heckler to injure them, and are willing to sit through a fourteen-hour production of Hamlet, so arguing with the same guy for half an hour until he gives up is nothing for them.
Garrus' loyalty mission:
If you confront Sidonis, he seems genuinely ashamed and guilty of his actions in betraying Garrus' squad. At first, this seems pretty normal for someone like that, but check the Codex entries on turians. Betrayal of the team and refusing to own up to your own mistakes and actions - like Sidonis did, by fleeing and hiding - is a deep taboo among the turians. No wonder the guy is so torn up about it.
Why does Garrus reluctantly forgive Sidonis? When confronted by his crimes, Sidonis confesses and owns up to his mistakes. That's another huge thing for turians, and ties into why Garrus chose to let him go.
Goes the other way for Garrus. Turian culture puts the stigma of a subordinate's incompetence, failures, or otherwise unsuitability on the heads of those who promoted them to that responsibility, as they made the mistake of putting someone in a position that they are incapable of handling or simply can't be trusted with. Garrus doesn't just blame the deaths of ten of the finest men he's ever worked with on Sidonis - it's common for officers in today's military to suffer severe psychological trauma upon their units taking heavy casualties. It'd be even worse for a turian. Thus, we have one of the major reasons why Sidonis' betrayal is eating so heavily on Garrus - to a turian, the treachery is as much Garrus' fault as it is Sidonis'. That's why taking out Sidonis is so important to Garrus, as he doesn't just want revenge, he wants absolution for his own errors in judgment. It's subtle, but you can see it in Garrus, both in body language and voice.
The Collectors and humanity:
They start to capture human colonists en masse to create a new Reaper based on humanity. This makes a lot of sense considering the Battle of the Citadel and Sovereign Nazara's destruction. With the Reaper fleet stranded in dark space after the death of their—presumably—only vanguard, a Reaper based on defiant and promising humans would be the perfect replacement and pave the way to the inevitable invasion. But Shepard comes back from death and destroys that too. Cue the pissed of Reapers powering up and charging headlong into the galaxy to unleash hell.
Not only that, but the novels drop a small tidbit about Collectors being interested in human biotics. This seems like a throwaway scrap of information, but it all makes sense when you consider they're trying to make new Reapers out of human genetic material. Reapers integrate biological material with element zero based technology. Biotics are a perfect group of subjects to see exactly how well the species is suited to this kind of synthesis. THAT'S the whole reason behind littering the galaxy with eezo-based technology too — they want to see how other species react to eezo to judge how compatible they are with Reaper technology.
Then you've got Cerberus, a human-supremacist organization with an unhealthy obsession for manipulating human genetics to make supermen, maximizing human biotic potential, and Reaper technology...and a newfound raging hard-on to kill Shepard according to Mass Effect 3's developers. Borderline Fridge Horror if you consider Shepard can deliver to them their very own Human-Reaper factory in the end of Mass Effect 2, and would then be the only person standing in the way of Cerberus constructing their own Reaper.
Plus, as far as can be told, the Reapers only harvest one or two species from each cycle into new Reapers. With the massive screw-ups that have plagued this cycle, why wait until the Reapers get there to start building?
So, hey, the credits are pretty nifty and all, with that awesome music playing in the background, as you're reading that white text against a black background with gold section headers... wait a second, where have we seen that color scheme before? That's Cerberus' colors!
Speaking of colors. The repaints after the loyalty missions all have the generic badass black color-scheme while the original outfits all had more originality and the colors made everyone seem more individual. Looking at the squad selection screen after getting several loyalty missions though you start to notice that the loyal ones are starting to look similar. As they become loyal they're putting on a uniform. They're becoming part of the team. The other team members go from various color schemes to some combination of black/orange/white. Garrus, and to a lesser degree, Tali, change their armors to something that resembles the Cerberus color palette, but maintains distinct differences, such as Garrus' use of blue. Yes, the ME1 veterans are changing something to fit in with Cerberus, but retaining enough individuality to show that they are allied with Shepard first, and Cerberus a very distant second. The reason that Garrus shows more individuality is that he was recruited early, when Shepard was at his most uncomfortable working with/for The Illusive Man.
Anyone notice the character models in the prologue are from the original Mass Effect - it's especially apparent with Joker. The new character models are shown off after the credits.
Legion's theme music contains hints of the Mass Effect 1 geth theme.
You know why Shepard dies if his/her entire team does? Because there's no one who can pull Shepard up after his/her leap to the Normandy. Joker is too weak and brittle to do it himself. Plus, the Collectors manage to shoot him - he's pulling Shepard up, he gets hit, and drops him/her (Shepard manages to hold onto the edge). This doesn't happen if two teammates survive: Joker keeps shooting, and one of your squadmates pulls Shepard up. With two people around, one of them is providing covering fire. When alone, only Joker is there and he's pulling Shepard. Joker pulling means he's not providing covering fire. Without covering fire to keep heads down, the Collectors can take their time to aim and actually hit something.
If the player chooses Morinth instead of Samara during the latter's loyalty mission, Morinth will join the squad. At the end of the game, you're given option to have sex with Morinth, but it obviously leads to Death by Sex. A common belief is Shepard would have to be stupid to have sex with Morinth but it actually makes sense in context. Morinth is a character who puts her victims in More Than Mind Control and has an absolute obsession with winning. Shepard is the one person who ever escaped her grasp. So essentially she was biding her time until Shepard finally fell under her control.
When you find out that Archangel is actually Garrus and he's been holding off wave after wave of mercenaries, mech soldiers, and elite hitmen for days, you might just assume that Garrus Took a Level in Badass, right? Except if you talk to Garrus frequently in the first game, you find out that he was originally hand-picked as someone who would make a good Spectre candidate. Of course he was able to take fifteen Levels In Badass in the sequel — he could have been the turian Shepard, and he's embracing his innate Spectre talents!
The name of the LOKI mechs is pretty funny when you realize that they're constantly glitching out and betraying you.
Legion and hacking:
When talking to Legion, Shepard mentions that the geth are immune to hacking. However, in what would normally look like a case of Gameplay and Story Segregation, the AI Hacking ability works on them just like any other Mecha-Mook. It isn't until you think about why the geth are hack-proof that it makes sense. Their programming acts like a giant wiki. If a couple of geth programs realize that some of the others are acting weird, they can just replace them with older, unhacked versions. The reload, however, takes time, which is why the AI Hacking ability only works for a few seconds, rather than permanently like it would with current-day computer programs, or not-at-all if the update was instantaneous. The non-geth synthetics have anti-virus software or internal backups which accomplish pretty much the same purpose. Who knew Wiki Magic could be used as a tactical advantage?
In the Shadow Broker's Dossiers, Legion is a huge gamer, not because they found it fun, but rather it was a means of Psychic Static, since the Shadow Broker keeps tabs on almost everything. One way for Legion to counteract that is to delegate a set of programs to be playing video games (from Grim Terminus Alliance to that Quarian Dating Sim), another set to combat function and the rest to deal with annoying AI intrusion, switched regularly of course. It was only during the whole conversation with EDI were they able to get a relevant log related to Legion. More than that, Legion used a video game to funnel significant funding towards the rebuilding of Eden Prime. Whether Legion feels genuine remorse at that point in the game or is just trying to distance the actions of the Heretics from the main body of geth is up to debate.
While Anyone Can Die in the second game, having any of your squadmates die doesn't actually affect the post-game much...except if Mordin dies, then all your upgrades suddenly require 50% more resources to get. You no longer have the brilliant scientist operating the tech lab, so of course getting upgrades takes more effort.
Mordin's loyalty mission:
The entire mission pushes his deep morality to the limit, especially if Paragon Shepard chooses to argue with him. What's his main justification for enacting the genophage? Judging an entire species by their reputation and biology. Hmm, what was one of the main points of the game? Oh right - you can't judge a person by their species or race, you have to take them individually. It doesn't completely invalidate his position, of course, but it does make it even more deliciously complex, even more so considering it's juxtaposed with Wrex's work.
The most shocking part is that, if pushed enough, Mordin gives his main reason for perfecting the genophage: The simulations did not show krogan immune to the genophage taking over the Galaxy, no, they did show turians and humans committing genocide against the krogan. Mordin did not act the way he did because he feared the krogan, but because he did not trust his very own civilization. And remember: Mordin says that turians and humans would have committed a genocide against the krogan: who's the best human warrior of his/her generation? Had the genophage 2.0 not been designed, chances are that either the Alliance, Cerberus, or both, would have tasked Shepard with slaughtering the krogan.
Also, between that mission and the Codex entries on Salarians it's disturbingly clearly that the Salarians used to genophage to reshape Krogan society to be like their own, with males competing for the right to mate, and with females having more power because of it.
Mordin in the suicide mission:
Mordin dies really easily in the suicide mission even if he's loyal, which makes a good share of the players rip their hair off. If you've talked to him often, you might have stumbled into a conversation where he mentions that he worked with captain Kirrahe who you encountered on Virmire in the first game. Mordin remarks, that while the captain's "Hold the line"speeches were impressive, he personally hates it. If you assign him to hold the line during suicide mission, there's a good chance he's a goner, but if you don't he survives (if he's loyal).
Meanwhile, his powers are all geared toward taking out individuals or small groups instantly, he moves fast, and he's not very durable. This makes him a perfect choice for moving rapidly through enemy territory, especially when they're distracted by you, but not particularly useful in an extended battle due to his lack of heavy weapons or armor and long cooldowns. He's perfectly suited, both in story and gameplay, to espionage and escort missions, while being less useful than any other character in a siege.
Beyond that, Mordin states he's in the last decade of his life, a fact that's reinforced by his decision to retire from the STG. He's old, and therefore less likely to survive severe injury.
Thinking about this further, it's evidence that the designers planned out every detail of the suicide mission such that you can't just check off the loyalty missions and expect everyone to survive; you need to actually be a good leader by learning your squad's strengths, weakness, and personalities and assigning them accordingly. It's pretty heavily hinted at in the game itself, as well - the crew has just been rescued, and they're probably pretty shaken up and at least a couple of them looked to be pretty badly injured during the Collector attack on the Normandy. They need a doctor. Chakwas is there, but she doesn't look to be in such great shape herself, either. What's that you say? You have a highly-skilled doctor on your team who's not suited to front-line combat?
Throughout the game, Miranda makes a big deal of how she was "designed to be perfect" and that hasn't really made her life significantly better. It's easy to take this at face value as An Aesop against the limitations and potential misuse of genetic engineering, but then you realise that there's a a double, out-of-universe meaning. Miranda is a Sentinel: she can use both Warp and Overload, making her effective against enemies with all four types of protection. Her passive boosts the entire squad's weapon damage and health points. Not to mention she also gets the most powerful Advanced ability in terms of raw damage. Slam can one-hit kill Collectors, and its cooldown is one second. And she's one of only two squadmates that can max out three abilities instead of just two. Biowareliterallydesigned Miranda to be the perfect squadmate.
It gets weirder. Remember how her only flaw was that she was infertile? Why would her father care if she can have children, when he can demonstrably make more of her if he so chose? Now, consider the next step: she joined Cerberus to get away from her father, who is later shown in ME3 to be a member. Her original duty in ME2? Resurrecting Shepard to be exactly as Shepard was before death, using technology that had to be exceedingly close to her own creation. It's even possible, depending on when her father was indoctrinated, that she wasn't designed to be "perfect" for humanity, her father, or Cerberus, but for the Reapers themselves: if they ever captured her, they'd unlock one of the most powerful biotics around and the cloning technology used to make her (and, therefore, the tech to make a reaper out of her alone).
You know why people don't respond in panic to the fact that you're bringing Legion onto the Citadel? Because A) Legion has a giant hole in them, B) Legion is wearing N7 armor, and C) It's in the company of Commander Shepard, a Spectre and war hero who saved the Citadel from the Reapers and would never do something like bringing geth onto the Citadel, or signing on with Cerberus, or bringing the rachni back, etc. etc. It's quite obvious that whatever Legion is, they aren't a geth, at least not after a moment's observation. Besides, maybe most people haven't actually seen geth, and most who have may be so traumatized that in their imaginations they are entirely different already. Whatever the reason, it's really funny to find that the tightened security couldn't in fact keep infiltrating geth out. Luckily, they don't infiltrate. ...Intentionally.
Why do Legion and Tali have the same powers ? Because the quarians built the geth, of course they are going to have the same base traits (Higher shield levels, tech-based skills etc.) Secondly, quarians hate the geth because they kicked them off of the homeworld. Their races aren't compatible, so the individuals aren't compatible. Meanwhile, putting multiple combat drones downrange means that enemies are unlikely to be shooting at you, their weapon selections are perfectly complimentary (shotgun and sniper rifle), Legion can tank with the best while Tali screws with enemy shields (assuming they're both loyal)... Throw in Squad Warp Ammo as your advanced training and even barriers aren't an issue anymore. They make a perfect pair if and only if you put thought into making them work well together and convincing them to get along.
The gameplay changes seem odd, until Jacob mentions that he wanted to leave the Alliance because they were too inefficient and never took action. The gameplay style affects who you're working for, so of course Cerberus will have you on missions that require you to take action more. And there's less RPG elements because everyone in your party either fought with you against Saren or has the traits or experience to account for what you gained from the first game. The only exception to this is Mordin, who because of this, dies the easiest in the suicide mission.
Afterlife and theme naming:
The nightclub Afterlife just seems like a random name for a bar/stripclub, right? WRONG. If you think about it, it gets its name from the mined-out space station it resides on, Omega. After all, the name Omega often alludes to the end of everything- life, death, whatever- and Afterlife is something of a beginning- at least to the mercs and scums who go there.
Shepard dies, comes back, and goes to Afterlife. To pick up Archangel.
And who rules Afterlife? Aria, voiced by Carrie-Anne Moss. Trinity. Like she says, she IS Omega and presumably the Alpha as well.
And in the comics, Afterlife was where Liara went to get your body in order to give it to the Cerberus scientists who would bring you back to life.
And then you go to Purgatory to pick up Jack. Purgatory is also where Aria is waiting for her chance to take back Omega. Purgatory is where those souls who aren't truly good or truly evil must wait and pay for their sins...before they can move on to the afterlife. It fits Aria on so many levels.
And later to help Miranda... you go to Eternity.
Miranda makes a great deal out of her genetic enhancements, complaining that a lot is expected of her and she doesn't view her achievements as her own because of it. A contributing factor to this is the extremes her father went to to ensure she was "perfect", up to and including disposing of those who weren't up to his standards. But this isn't the real reason. In the Lair of the Shadow Broker DLC, you get access to Shadow Broker dossiers on your squadmates which reveal sometimes hilarious and sometimes terribly sad facts about your squad. Miranda doesn't hate her genetic enhancements because of some (misguided) sense of worthlessness; she hates them because it might be the reason she can't naturally have children. A lot of people thought this was just was wangst and the tired old cliche of So Beautiful, It's a Curse - looks like they might have been wrong.
At the conclusion of the game, Harbinger speaks directly to Shepard for a few moments. “Human, you've changed nothing. Your species has the attention of those infinitely your greater. That which you know as Reapers are your salvation through destruction. You have failed. We will find another way. Releasing control.” At which point it's revealed that Harbinger wasn't the Collector general but rather the Reaper controlling him like the others. That last bit about having failed has always seemed like classic pointless villain chest pounding, though, especially since Shepard is inside the Normandy at that point and can't hear it. However, there's a second reveal hidden behind the first - at that point the Reaper isn't trying to intimidate you, it's not speaking to Shepard at all. It's speaking to the general, admonishing him, a final insult from his god before his death.
The background of the menu of Mass Effect 2 is the interior of the Normandy. The menu is Kelly's station. Combine that with full access, Cerberus Network terminal, TIM's reports to some PTB as mission conclusions, the fact that the gameplay itself is a record (as evidenced by the "film grain" effect) and the fact that Kelly was hand-picked by TIM for extra paranoia. And that DLC you download from EA's Cerberus Network? More gifts from the Illusive Man.
Remember the song 'The Attack', which plays during the Normandy's destruction in the prologue? It plays several more times during key points in the main storyline. It plays whenever the Collector ship appears to the point that it's practically a leitmotif for the Collectors, and picks up bigtime during both fights against the Praetorians on Horizon and the Collector Ship. Excluding interference with the Cain, the fights are extremely hard, even if you do have the right skills to destroy their Armor and Barriers. Finally, it plays when you fight the Human-Reaper Larva. The song evokes the bitter memory of frustration and hopelessness as you see the Normandy get sliced up around you. And now you're facing against a non-stop horde of Collectors and a Reaper, one of the Big Bad who orchestrated the Normandy's destruction and Shepard's death. Once the song plays again, it mashes the Berserk Button the game was conditioning the player into from the very beginning. Not only that, but the Collectors now drop tons of thermal clips and heavy weapons ammo, giving your hatred no limit to properly exact your revenge.
In the hold the line part, one would not expect an assassin like Thane to last like his biotic companions, but Thane is one of the last to die if the team's "hold the line" score doesn't pass, for a few reasons. He has a natural damage boost which makes him very formidable against organic foes and has an ammo power that makes hitting organic enemies even harder (Either against a single target or suppressing fire). And his religious devotion which include a goddess who he prays to for defense makes him a good candidate for holding the line. Thane is also a sniper— sniping is an excellent defensive fire tactic. Plus, he's a stealth expert - even if everyone else bites it, Thane will be perched up someplace that the Collectors can't find him, plinking them one at a time. Thane's skills are completely anti-Collector, to boot - sniper rifles are good against armor, submachine guns are good against barriers, and his biotics will tear right through Collector barriers. As mentioned his ammo power increases his damage against health. The guy was brought in for the sole purpose of eliminating Collectors.
At the end of Garrus' loyalty mission, if you're going with the Paragon route, when Sidonis talks about how he can't sleep at night, he walks to one side, and Shepard walks between him and Garrus to prevent Garrus from shooting him - until Sidonis leans against a railing. Pay close attention, and you'll notice that Shepard isn't next to the railing. He's giving Garrus a shot, and Garrus isn't taking it. After that, there's one last dialogue choice before Sidonis leaves, where Garrus wants one last chance to shoot Sidonis - even though he already has a clear shot. Garrus is putting some serious thought into this decision.
The green circuit board shown during the bypass minigame may seem like a decorative frill, until you figure out that all the links follow the electric circuits shown on it and never deviate from this template. Once you learn the internal logic of their layout, it becomes possible to win it every time without ever double-checking what symbols are actually hidden underneath the selectable dots or making any errors.
The reprogramming vs. destroying of the Geth Heretics seems to be a bit off on the morality scale. The renegade option has you simply killing them, while the paragon option has you brainwashing them! What the hell? Then, if you think about it, while paragon vs. renegade seems to be nice guy vs. jerk, it's actually more complicated. The result of Paragon actions tends to be less power concentrated in the hands of humanity, but more allies garnered for your side. The Renegade option tends to alienate or destroy any potential allies, but concentrate more and more power in humanity's hands. Therefore, reprogramming the Geth Heretics is clearly the Paragon option, because it turns a great enemy into a potential ally, while the Renegade option simply removes a threat. Also, if you listen carefully and explore all the conversation options with Legion, it becomes clear that releasing the virus won't force the Heretics to come around to the rest of the geth's way of thinking. Instead, it just creates a compulsion in them to return to the geth homeworld and integrate their experiences with the rest of their race. So really, all you're doing is forcing the Heretics and the geth to come together and confront their differences and build a consensus.
The 'biotic god' volus is actually a powerful biotic due to the drugs the Eclipse gave him, they're just not stupid enough to give him a biotic amp.
Why do you only get the Harbinger codex entry on the Renegade entry? That codex entry is the first of the rewards that you reap from keeping the Collector Station.
When you first encounter the Collectors in battle on Horizon, they seem to be little more than generic identical Mooks blindly rushing into battle. Then it is revealed later in the game by Mordin and EDI that the Reapers engineered them to be exactly that: Expendable servants with no sense of individuality and self-preservation. Just like any other type of husk.
During the final boss fight of Overlord, geth pop out of thin air to slow you down. At first, it just seems like they're there to stall you from a gameplay perspective, and wouldn't make sense in-universe. However, a few minutes earlier, David hacked your omni-tool and is basically controlling you. The geth also vanish when they die, implying they don't really exist. They do exist, and they are real geth - they're not geth platforms, they're geth programs. David is sending the few geth programs remaining on the planet to Mind Rape you via your omni-tool.
In Lair of the Shadow Broker, Liara starts with all four powers unlocked. This isn't just because she is only on your team for just this set of missions. This is because Liara has always been loyal to you.
The chef selling ramen noodles as a 'delicacy' seems like a quick jab at people taking advantage of tourists by fooling people into thinking something's worth more than it is. However, when you think about such delicacies as lobster and escargot, they both started as food people only ate when they were too poor or desperate to get anything else, so maybe he's telling the truth?
A minor bit of Fridge Brilliance: Joker's throwaway line about "plugging in the Overlord" isn't a case of Harsher in Hindsight given the Project Overlord DLC... it's actually an indicator that canonically, Shepard deals with Overlord before they try to use the Reaper IFF. Joker's not giving some unintentionally prophetic line, he's cracking a tasteless joke about a past experience, because Joker's stressed out and he's just kind of an asshole even at the best of times. Supported by talking to him after the fall of Thessia in Mass Effect 3, where he cracks a tasteless joke to Shepard about how the asari must be wishing they had more commandos instead of dancers right about now.
When you're giving EDI access to all of the Normandy's controls, Joker mutters, "Now I'll be spending all day computing pi because I plugged in the overlord." Obviously, this refers to how AIs are thought to conquer organics without a second thought, but it has a second meaning. In the final battle of the Overlord DLC, if you take too long, David will upload to the Normandy and take over EDI, who has full control over the ship. In effect, the Overlord was plugged in, and Joker is now useless, relegated to computing pi and the square root of 912.04.
There's actually a fair bit of logic in the abilities of your squadmates in ME2. Garrus was your Infiltrator swap in ME1, so he has a combat ability and a tech ability. Thane is an assassin, so he has the biotic abilities dedicated to killing people, instead of crowd control. Miranda was bred to be perfect, so she's the only squadmate who can take down all four forms of defense. Mordin is a scientist specializing in organics, so he has the two tech powers useful against organics. Tali grew up with a father who wanted war with the geth, and thus has abilities that take down shields and hack synthetics— two things very useful in a fight against the geth. Legion is a geth, so his powers consist of using his many runtimes to either hack other robots or to provide fire support. He's also a sniper, so having a drone to provide crowd control would be very helpful. My two favorites however, are Zaeed and Jack. Zaeed has spent most of his life trying to take down the Blue Suns. As any Adept will tell you through gritted teeth, the Blue Suns all use Shields. So, it makes perfect sense that he's the only squad member who can use disruptor ammo, which is specifically designed to take down shields. Jack is the absolute best, so just stay with me. Some people in the ME universe consider biotics to be an evolution of humanity, some kind of higher form of existence (think mutants from X-men). In other words, to use Harbinger's words, biotics are humanity's GENETIC DESTINY. Harbinger constantly taunts Shepard with those particular words, and it is eventually revealed that his idea for humanity's genetic destiny involves either being turned into a Reaper or becoming a slave race like the Protheans. Jack is the most powerful human biotic in the galaxy. In other words, she has already reached humanity's genetic destiny; she is a higher form of human... sort of. So, whose powers are the absolute best at fighting off the agents of the Reapers? Who is best at preserving humanity's own genetic destiny and staving off the destiny that the Reapers had in mind? Well, with Shockwave (best move for taking down husks) and Warp Ammo (specifically designed to take down barriers, armor and health. If those sound familiar, they are the only form of defense that the Collectors use), Jack is the absolute best squadmate to take on the Collector missions in the game. Hell, Harbinger doesn't even stand a chance against humanity's own genetic destiny.
In Grunt's recruitment mission, you get to meet a tank-bred krogan who helps you defeat the Blue Sun mercenaries. Notice that when the krogan confronts Shepard (ie. you) face-to-face, his head is right about the height of your chest, making it look like he's looking at your tits, if you're playing as a Fem!Shep. But then Fridge Brilliance kicks in: he's is only a week old! Of course he'd be shorter than any of the krogan you have ever met!
Fans might be disappointed that Seth Green didn't reprise his role as Joker for the Arrival DLC. He's completely silent whenever he appears, and even when the Normandy arrives at the end the voice on the comm isn't him. Thinking about it though, it makes sense. At the very least Joker knew he was saving Shepard from an asteroid about to smash into a mass relay, something that is depicted as a rather grave event. Depending on how much s/he tells him he might also know about the Reapers and how they were minutes away. Whenever things get serious Joker goes all quiet, so they could get away with the Deadpan Snarker becoming The Voiceless.
Check out Sentinel’s Biotic abilities in ME2, Warp and Throw. What do they have in common? They get made more powerful from other abilities, Warp detonates Biotic abilities and Throw hits harder if your enemy if floating from pull or something like that. But they don't have the ability to take advantage of these abilities, especially noticeable when so many biotic abilities can be used, making them seem poorly chosen. However, Sentinels are designed to be team players, they make their team mates more effective, by stripping your enemies defences but their team mates, make the sentinel more effective too. Along these same lines, Sentinels also have a limited weapon selection, but Tech Armor, making them great tanks for the team, but the damage output is weakened, thus fitting them into the team mentality even tighter.
In Mass Effect 2, some people may wonder why, if Shepard ends up being unable to resist Morinth in Samara's loyalty mission, that the cutscene between her and Samara that immediately follows plays out in the same fashion, with the only difference being Shepard automatically chooses to aid Samara. Why don't you get the choice? Because Shepard cannot resist Morinth, and realises that if s/he lets Samara die, Morinth's way of thanks would be to immediately put on the moves, seduce Shepard and kill him/her. Even a Renegade Shepard realises this, and though Samara may be a future problem, right now the bigger danger is the hypnotic sex vamp. That also explains why you need a maxed out Paragon/Renegade bar to make the choice in the first place - only the most badass Shepard can resist Morinth and bring her to heel.
If you ask Jacob about what's missing on the Normandy, he often complains about the lack of a bar. Kasumi's personal quarters has a bar and entertainment lounge to it. And her haikus are all focused on Jacob. By setting up shop in there, she's forcing him to come to her if he wants a drink.
We went from having individual cooldowns for different abilities and powers, to a global cooldown from the use of any one power. But all the powers and abilities in Mass Effect 2 have been greatly improved. Everything from their functionality, overall power, and especially their cooldowns greatly overshadows the abilities in the first game. So much so that they would require greater focus and energy, and make it impossible for the user to be able to muster up the strength to safely perform another action. Possibly even further, that focus is not gone, but being used quicken the cooldown overall. Thus, greater combat presence at the cost of a global cooldown.
So, why is it that it appears that Humans Are Special now? Well, they weren't until Shepard came along. Originally, Saren made turians the candidate by working alongside Nazara. Then Shepard showed up, kicked his ass, and got Nazara killed. By humans, no less. At this point, the reapers made the practical decision of picking humans instead, after they obviously showed their dominance. Then, to add to that, Shepard died and came back, and fucked up their plans even more. Humans Are Special because you made them special. It also points out a major flaw in the Reaper's philosophy. Their supposed "existence beyond comprehension" makes it impossible to for them to see the worth and potential of an individual. When they see Shepard take out one of their own, they attribute it to humanity's genetic makeup, rather than Shepard's own determination. Hence why they were trying to build a Reaper out of humans in ME2. But we know from Miranda and Grunt that having perfect genes isn't all that it's cracked up to be. Miranda even says outright that Shepard has something that she could never emulate. The aesop Bioware seems to be going for is that experience determines ability, not genetics, which is something the Reapers still don't seem to understand. Shepard could have been a krogan, turian, quarian, asari, or whatever, and s/he would still be just as Badass as ever.
Wrex is uniting all of the krogan tribes under his rule. Which takes on a new meaning when you remember 'Rex' is Latin for king.
Shepard can keep a fish tank in his/her quarters. You have to feed them after every mission you embark on to keep them alive. In other words, they have a lifespan of a single mission before they die without Shepard's intervention. Guess who else is in that same situation by the end of the game? The Normandy crew after being captured by the Collectors. If you spend time talking with Kelly Chambers (ie gaining her loyalty), at one point she can help out with the fish care duties, enabling Shepard to focus on bigger issues. Just like how those squadmates you talked with and gained their trust and commitment contribute in the Collector Base, enabling Shepard to focus on bigger issues.
When scanning the planet Jacob's loyalty mission is on, there's a massive deposit of element zero right at the location of the crashed ship. At first it seems unusual, since element zero is usually found only on the "post-garden" planets, but then the fridge brilliance kicks in: it was coming from the ship! The scanner was picking up the the eezo in the ship's core.
Warden Kuril's name in Mass Effect 2. "Cure ill." -> what he imagines himself to be doing.
Notice the wall designs of Afterlife. Fire holovids. After all, you are in hell — literally.
Lots of talk about how stupid it was to leave the Reaper artifact just lying about in Arrival, but think about it a moment. Who would have been the first people to fall to indoctrination? The people who spent the most time around it, ie the people responsible for making sure it WASN'T just lying about.
After doing a couple of side quests for Liara on Illium, you get the option to tell her to not 'turn into the thing you're hunting'- referring to the Shadow Broker. Well, let's just say it's really ironic...
Food for thought; how many of Archangel's squad were killed because of Sidonis's betrayal?. Ten. Discounting DLC, how many squad members put their lives in Shep's hands during the suicide mission? Ten. And think about it; we know that Garrus was considered for Spectre status, but turned it down. Tragically, it's like he constantly fails at trying to be like Shepard.
And unlike Garrus who is unable to prevent Sidonis from turning on him, Shepard is able to convince Wrex not to turn on him/her in anger on Virmire.
Why did Archangel fail in his mission to clean out Omega? Because he didn't gain the loyalty of his entire squad.
It's safe to say that Shepard is Garrus' Foil- especially if Shep is a paragon. Note that the Shadow Broker's dossier on Garrus essentially says that he is actually being stunted in his development as a leader by being under Shepard's command.
The next time you recruit Garrus, check around the base. See those covered dead bodies? Those were his squad.
You can actually tell the story of the squad by their placement. On the upper floor are two covered bodies; if you talk to Garrus after the mission he states that "when I got back there were two left... and they didn't last long". Downstairs are the bodies of the remaining team, organized rather nearly in a row; this implies that they dragged their comrades to the same spot as they gradually fell during the attack. But the ones upstairs aren't aligned at all, which implies that they were pushed upstairs due to lower numbers, and that Garrus effectively had to chuck some covers over them and get back to fighting after he found them.
If you're a particularly poor (or intentionally bad?) player, the corpses of Garrus' squad mirror the sheer body count you can rack up during the suicide mission. That Garrus comes back to find only two of his squad alive can also be compared to how Shepard needs two squad members alive to survive the suicide mission.
ME2 has a huge theme of death, life and resurrection:
Shepard died and is resurrected at the beginning of the game.
The Normandy dies and is resurrected. Both were resurrected by Cerberus. In Greek mythology, the Cerberus, a three-headed dog, guards the gates of Hades. So one could infer that Cerberus wouldn't let Shepard or the Normandy pass the gates of Hades.
The first place Shepard goes to of her/his own volition is Omega, to Afterlife. To pick up Archangel and a doctor. Omega is the final letter of the Greek alphabet, the end. Make of that what you will, but Omega is known to have a pretty high death rate...
Garrus—when you first pick him up he's killing people. Not that unusual, except he's probably the only one apart from possibly Thane who's actively killing people while you're getting his quest. Also, his vigilante name is Archangel.
His loyalty mission deals with Sidonis, the traitor of his twelve-man team, who was attempting to build a new life for himself on the Citadel. Regardless of whether or not Garrus does ultimately kill him, it is the end of Sidonis' new life. Even if he lives, he turns himself in for his crimes.
Mordin—an elderly doctor who kills people. Kind of a paradox.
His loyalty mission is about him discovering his student was trying to reverse the genophage modification, which would allow all krogan females to be fertile, to bear life.
Jack—has an enormous omega symbol on her back. Also, she's cryogenically suspended. Not permitted to live, but not permitted to die either.
Her loyalty mission has her returning to the place where she was "born" as Subject Zero, and erasing it. Shepard can also convince her to spare a fellow victim of the facility as a way for both of them to move on with their lives.
Samara—"Appointment in Samarra." In the original story, Death is a woman.
Her loyalty mission has Shepard helping her hunt and corner her daughter, who kills through mating.
Grunt—tying into the life theme, Grunt is the youngest squadmember, and he's practically a child compared to the other krogan Shepard meets. Also Grunt is born on the Normandy. In a sense, by Shepard him/herself.
His loyalty mission is about him finding purpose, a life of his own, outside of Okeer's intentions for him.
Thane—a dying assassin with a young son.
His loyalty mission has him attempting to guide said son (Thane himself describes him as "his body and soul are disconnected") into the right path and away from assassination.
The krogan and the quarians—both races trying to restore (to resurrect?) themselves.
The Reapers in general—the ultimate death dealers, but it seems that they kill to create life.
Miranda's father engineered her to be "perfect". He wanted her (and/or her twin sister) to be the first of a genetic dynasty. In other words, he wanted a kind of immortality.
Several moments, when you listen at the music:
The background music during the biotic walk has a part at 2:37 that sounds almost exactly like the part at 5:48 of Samara's theme. At 1:05, the overall Mass Effect theme starts playing... using the instrumentation from the slow plodding march at the beginning of Jack's theme. Guess which characters are excellent choices for that section?
The track called "Infiltration is played at three separate points in the game: during Tali's recruitment mission (fighting the geth drones), Legion's loyalty mission (holding the main room against a geth onslaught), and the vents run on the Suicide mission. Guess which two characters (barring DLC) are ideal candidates to run through the vents.
Also in ME2, the song that plays during the exploration of the Collector Ship is also played during the Normandy Crash DLC, and when you free the survivors from their pods. The song is for all the people that the Collectors have killed or captured.
Why did Wilson go so far with the mech reprogramming at the Lazarus facility? Because he's trying to murder Shepard in the middle of a lab designed to bring the dead back to life. Shepard is brought in as a charred corpse and successfully resurrected, so no amount of drugs, poisons or even bullets would have worked - they'd have patched Shepard right up. In order for the murder to really take, he had to destroy everything: the staff, the notes, the tech, all of it. Only by razing the entire Lazarus project to the ground would Shepard truly be dead.
After you complete Aria's mission to help the Patriarch (either by giving him newfound confidence in himself or talking him into a suicide charge) she rewards you with info on a planet with stolen goods. Three YMIR mechs await you there, trying to smash the goods and Shepard as well. No matter how many times I played the game, I can't decide if this is Aria's way of rewarding you or trying to kill you. This fits Aria perfectly, of course.
Alternatively, Shepard survives (like he/she always does somehow), but the smugglers manage to destroy at least a good number of the goods before Shepard can get his/her hands on it. In other words, Shepard and squad traveled all that way, used all that fuel, risked their lives, used all that ammo, and wasted all that time for a reward that wouldn't have covered the expenses. Maybe a little too passive-aggressive for Aria, but I can see her having a good laugh if that's what happens.
The Thanix Cannon was reverse-engineered from Sovereign, making its use against the Collectors deliciously ironic. That's not the Fridge Brilliance part. That would be the fact that you get the upgrade from Garrus, who loves to inflict Hoist by His Own Petard upon his opponents. They really thought this through.
A big reason why Tali's mission on Haestrom was such a bloodbath was because its layout is exactly what quarian soldiers are not trained for; wide-open spaces where staying out of cover for too long fries your electronics (including shields, which the quarians rely on for defense). They fare slightly better when hiding behind bottlenecks such as tunnel entrances, but without long range weapons they can't attack the geth until they get up close (Kal'Reegar was the only one we saw with a ranged weapon, and he was the leader). The geth, on the other hand, have plenty of ranged weapons like rocket launchers and sniper rifles (not to mention that colossus with the self-repair program), which would make the quarians easy pickings when they're all holed up in one place.
The fact that shields are completely useless on Haestrom because of the sun is Fridge Brilliance in itself: One can recall having Tali as a squadmate in ME1, she has the strongest shields in-game, making her virtually invincible if you build her stats right. This is to make up for her being a quarian; they can't wear medium or heavy armor, so they make up for it by integrating components on their hardsuits that strengthens shields. On Haestrom though, this backfires: because of the radiation exposure from the system's unstable sun, shields are useless and therefore make the quarian team easy pickings for the geth.
Why aren't the geth you fight affected by the shield-destroying solar radiation, even though your party is? Simple! The Geth Shield Strength upgrades exposit that geth use very different, technologically incompatible shield systems from everyone else - and the ones with the best hope of recreating their design, the quarians, would mostly use recycled Citadel species tech in order to ease integration of salvaged components. Clearly Geth shield technology is more resistant to the radiation coming from Haestrom's sun. As for why Legion is affected (assuming this is the case; haven't tested it), given that Legion's platform has a whopping great chunk blasted out of its chest, it could be that the onboard shield emitters have been damaged in such a way that this resistance no longer applies.
Why do the Collectors shift into high gear after Sovereign is destroyed? Because they're going to use the Human-Reaper to open up the Citadel relay. The Reaper fleet doesn't activate until the end because they were waiting until the relay could be opened - and that isn't an option anymore.
So a badass sniper assembles a merry gang of people and it all goes swimmingly until he's betrayed by someone from within. He gets shot in the face, decides against dying from it, but wears both physical and psychological scars from the whole debacle. Oh, and he asks Shepard to help him track down and kill said traitor so he can focus on the mission. Basically, the only difference between Zaaed and Garrus is that Garrus had much more affection for his squad than Zaeed ever did for his, to the point of blaming himself for trusting Sidonis enough to let the other turian do what he did. Similar things happen and they both want Shep's help in getting revenge, but Garrus feels responsible for the people he led, even the traitor, and needs barely any nudging to recognize that it's wrong to hurt unrelated people in pursuit of revenge. Zaeed's motives are a lot simpler and more basic, and he doesn't have that empathy.
Why was the Shadow Broker so willing to work with the Collectors? Simple: he was thinking like a Yahg. It's said they serve those who firmly establish they're stronger with fearsome loyalty. The Collectors simply established their dominance, and the Shadow Broker dared not challenge it.
The named relays in ME2. The Collectors are behind the Omega 4 Relay. The Reapers are trying to arrive through the Alpha Relay. The Alpha Relay is the beginning of the Reaper invasion. The Omega Relay leads to the end result of their invasion.
The "Fight for the Lost" slogan that was used in the advertisement for the second game, not to mention some of the plot, has some bizarre thematic parallels with this;
Ezekiel 34:12-16: As a Shepherd looks after his scattered flock when he is with them, so will I look after my sheep. I will rescue them from all the places where they were scattered on a day of clouds and darkness. [...] I will search for the lost and bring back the strays. I will bind up the injured and strengthen the weak, but the sleek and the strong I will destroy. I will Shepherd the flock with justice.
In ME2, when you visit the Migrant Fleet, you learn that the quarians insist on calling Shepard "Captain" Shepard, based on their own customs due to him being the captain of his ship, despite his human rank being "Commander." This is a mark of great respect amongst their people. Admiral Xen, arguably the least sympathetic of the Admirals, is the only quarian who doesn't know you from elsewhere that refers to you as Commander. Snub on her part?
Why does a Paragon Shepard disapprove of Zaeed so much during his loyalty mission? His strategy - set a refinery on fire as a distraction - is the exact same one that led to Anderson figuring out Saren was rotten.
Wrex's comment when meeting him about hearing about Shepard and respecting him/her gains a lot of weight in ME2 with the Sole Survivor backstory.The initiation into adulthood ritual of Clan Urdnot, Wrex's clan, is to survive going up against a single thresher maw. With Sole Survivor, you do that.
The lovestruck krogan and his asari paramour. During his fits of poetry, he calls her the "Blue Rose of Ilium". Blue roses don't occur naturally, just as their relationship would not have. Blue roses are also symbolic of the unattainable and mysterious, and show desire for goals you cannot reach. They are also used to say "I can't have you, but I can't stop thinking about you." Intentionally or not, he wasn't just commenting on her skin color and beauty. He was making her into a symbol of everything he wanted but didn't think he could have.
In ME2, Kasumi (and the Shadow Broker) are the only ones that use omni-tool based weapons. The Broker busts out an omni-shield and Kasumi has her Shadow Strike ability. Both of these make perfect sense for their characters. It's mentioned on the Fridge Logic page that until close combat with Husks became a thing, everyone regarded the omni-blade as a fool's weapon. Well, let's see. Who never leaves their quarters/control room and only expects to be fighting on their own turf with terrain designed to support a one-way shield? The Broker. Who needs to quietly take down someone (say a guard) without necessarily killing them and without setting off an alarm in order to steal something? Kasumi.
In ME2, there is a news report that the hanar believe the kidnapping of human colonies is some sort of vengeance by the Enkindlers (A.K.A. the Protheans) for destroying the beacon. Though this may seem like comic relief, in a weird way they are right. For starters, the Reapers may not have developed as much interest in humanity had Shepard not discovered the beacon and saved the galaxy in ME1. Then in ME2, you find out that the collectors are modified Protheans and it seems a lot more like foreshadowing...
Call it contrived if you want, but the abduction of the crew proves to be quite convenient for minimizing random crew casualties during the journey to the base. If there were crew members there, there would also be a strong chance of losing random crewmates on route (from the Oculus or simply from random damage to the ship), which defeats the meaning of "No one left behind". Plus it's really convenient for Shepards who are looking to romance Miranda; no dirty comments from Donnelly after you did it with her.
Jacob gets a lot of flak for being "boring," being comparatively balanced compared to the rest of the crew having semi-permanent residence on Dysfunction Junction. His loyalty mission comes and goes without much fuss. Then you do the Shadow Broker DLC and the Broker notes that Jacob was clearly placed on your team as a stabilizing element. He was supposed to be relatively dull.
Take a look at the first batch of characters Shepard recruits in the game: Miranda (an incredibly skilled and well trained human Sentinel), Jacob (a skilled Alliance soldier with family problems), Mordin ( a tech expert who's far more deadly than he seems), Grunt (a badass krogan who could make a real difference to his people), Jack (a massively powerful biotic who is being held prisoner and must be rescued by Shepard) and Archangel (a badass turian dedicating himself to wiping out crime). Look familiar? let's look at Shepard's squad from the first game: Kaidan (an incredibly skilled and well trained human Sentinel), Ashley (a skilled Alliance soldier with family problems), Tali (a tech expert who's far more deadly than she seems), Wrex (a badass krogan who could make a real difference to his people), Liara (a massively powerful biotic who is being held prisoner and must be rescued by Shepard) and Garrus ( a badass turian dedicating himself to wiping out crime).
Why can't you romance Garrus in 2 if you didn't pick him up in 1? Think about how FemShep tells Garrus she's not interested in Jacob: "I don't want someone closer to home...I want someone I can trust." If you didn't have Garrus in the first game, he hasn't earned that trust!
There are quite a few counter-points in the course of the main story, where a renegade Shepard essentially becomes quite like Saren - cybernetic implants, glowing eyes, the option to let a refinery full of civilians burn in the name of completing the mission (see above). What Shepard is forced to do in the Arrival DLC is essentially a scaled-up version of what Balak tries to do in Bring Down The Sky. The reasons are different, sure, but it's the Not So Different moment for the DLC.
Miranda's reasons for quitting Cerberus in order to destroy the Collector Base are obvious. It's a monstrosity and no one, not even the Illusive Man, can be trusted with it. But depending on how you play your Shepard, there is another reason. In conversations with Miranda, a Paragon Shepard will constantly tell her that her genetic engineering doesn't make her great. Even if Miranda doesn't believe it herself, it appears as if that's the first time she heard that from anyone. Her father was strict and isolationist in terms of her upbringing and the Illusive Man had told her that her genetic engineering are what make her valuable and a promising operative. In other words, while others had only seen her for her artificially induced talents, Shepard is the first person to see her as a real person whose strength comes from her own personality and decisions, in spite of knowing her origins.
You know that scene in the beginning where Shepard wakes up partially? With Miranda and Wilson panicking and trying to sedate him/her again? And Miranda says Wilson underestimated the amount of sedatives necessary? Yeah, Wilson just made his first attempt on your life.
There are multiple indicators that Wilson is the mole: His money troubles, how dismayed he was at your survival, and he lets slip that the bots are "going crazy and trying to kill him". No single conclusive piece of evidence, but taken together, they're quite obvious.
If you were lucky to do the 'N7: Archeological Dig Site' mission on the planet Joab before the The Reveal, you'd discover yourself that the Protheans portrayed in the vision/massacre/flashback Shepard sees are Collectors... the Protheans ARE the Collectors! The Horror! The ending of the second game does in fact explain the strange visions Shepard gets shown from the beacons in the first game. When you play the game for the first time, it looks like flashing images of random gore, but given the knowledge of how Reapers are created, the images appear to show the Protheans getting torn apart and remolded on the mechanic parts of a new reaper.
There's a mission in ME2 where the Blue Suns mercenaries are raiding a starship. In one room, Shepard finds two Blue Sun turians who are not helping any of the teams dispatched to stop Shepard. There aren't really any valuables in the room. There's nothing too noteworthy... except a pile of six or seven somewhat burnt, completely unclothed humans. Man, those Blue Suns sure are murderous - wait, unclothed, burned human corpses? What you've thought cannot be unthought. However, they were probably just stripping and cremating them. Like Nazis. That's much better, right?
In the Shadow Broker DLC for Mass Effect 2, you can read dossiers on your crewmates. Of particular interest is Grunt's, which shows that he's developing a taste for Ernest Hemingway's work. However, he seems to have read and then deleted the novel A Farewell to Arms. Seeing as he's a member of a warrior race, you might think it's because of the title. It's not. At the end of the novel, the main character's love interest gives birth to a stillborn and then bleeds to death. Given what we know about the genophage, that imagery probably hit a little too close to home for poor Grunt.
If you let the timer run out in The Arrival, you get treated to a Non-Standard Game Over montage of the Reapers arriving and taking over, in a series of quick cuts that make it hard to tell what is going on, with a heavy red filter on everything. Looks a lot like the message the Protheans left behind the last time around, huh?
Looking at most of the non-DLC squadmates in Mass Effect 2 can prompt a bit of this. The first batch of dossiers TIM gives you? A super-powered biotic, a highly knowledgeable krogan warlord (replaced by a super-krogan with Collector tech), a skilled vigilante, and a former STG operative and incredibly intelligent doctor. Barring Garrus, all of them are people that TIM would want to utilize for Cerberus (whether through dissection, picking their brains, or using their skills), not just for the suicide mission. He's got you on a recruiting mission for Cerberus. Even the ones that couldn't be used or experimented upon for their skills are possible recruited assets - TIM would probably prefer that you don't rein in Garrus or help Thane with his issues, because two Cold Sniper assassins would be incredibly useful for Cerberus, as would a highly successful merc, and the best thief in the galaxy. Tali and Samara are disposable resources, useful for the Suicide Mission but easily disposed of after. Plus, a biotic as powerful as Samara would make for an interesting dissection, and at the end of Samara's loyalty mission TIM even says Morinth would have made a useful asset.
The reason why everyone you pick up (except for Jacob, who is assigned to you, not someone you recruit) is in the middle of the Dysfunction Junction? Because they are potentially useful assets who Cerebus does not consider worth the time to otherwise recruit: in other words, people who Have Outlived Their Usefulness to Cerebus before even being recruited, and are considered people who Cerebus doesn't care about and, in some cases, might actively want dead (like Jack). Cerebus has decided that these people would be useful Meat Shields for Shepard.
Cerberus created Jack as a super weapon. They've been chasing her ever since she escaped from the Pragia but she hates them intensely and has massive trust issues so their operatives can't get close. But then along comes Shepard who needs her for his mission and wins her trust....while keeping her on a Cerberus ship filled with Cerberus agents and the supposedly unwaveringly loyal Miranda. If Miranda had stuck with Cerberus she probably would have received orders to incapacitate Jack and return her to Cerberus as soon as Shepard was distracted. In fact, since the Illusive Man sends you the dossier for Samara after you've recruited Jack it's possible the only reason he sent Shepard to pick Jack up at all was as a smokescreen for kidnapping her.
All those guards you singlehandedly bulldoze through during the Arrival DLC? Yeah, those are most likely indoctrinated scientists and researchers. No wonder they barely have time to squeal before Shepard splatters them all over the walls.
Miranda says that she wasn't her father's first daughter, just the first one that he kept. Did he cull the others before or after birth? How long before or after birth?
You can find Shepard's helmet on Alchera. Which begs the question... how did Shepard's helmet get separated from his/her head? Or rather, did his/her head get separated from his/her body? That would put a whole new spin on how much effort Cerberus had to spend on reconstructing Shepard's corpse if they had to reconstruct your entire body from bits scattered across the Normandy crash site....
One of Mordin's comments on the Citadel mentions he wishes he had studied the Keepers, but he always had other more important things to do. Think about that. If Mordin hadn't been recruited to do STG work, he might have completed Chorban and Jhaleed's work much earlier, learned the truth about the Keepers, and warned everyone about the Reapers... or even more worrying, he could have published his findings, and pushed Sovereign to attack earlier than planned and bring the Reapers in years beforehand.
On Pragia you can acquire an upgrade for biotics from a chair with arm and leg restraints. Given the nature of the facility, it's pretty much guaranteed that one or more children were tortured to get that information and now you're benefiting from it.