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    Fridge Brilliance 
  • After defeating Saren, Shepard is given three choices: Save the Council and Destiny Ascension (Paragon), leave them to die (Renegade), or concentrate on Sovereign (Neutral). The neutral choice gives Shepard both Paragon and Renegade points, because they are focusing solely on the main problem to the exclusion of everything and everyone else (a Renegade solution), while doing so for practical rather than petty reasons (hence the Paragon points).
  • The loading screens that depict the Normandy travelling between systems - displaying its built-in FTL drive with the red light heading "toward" the Normandy and the blue light heading "away" from it – seem like just a cool effect. However, if you reread the Codex's entry on FTL drives, you realize the light "approaching" the Normandy was being red-shifted by the mass effect field (to an observer inside the mass effect field, everything outside is red-shifted), and the light moving away from it was being blue shifted (an observer outside the field would see everything within the field as blue-shifted), exactly as it was described in the Codex.
  • Manuel from Eden Prime may seem crazy at first, but on hindsight, everything that he babbled about was actually true. He was probably exposed to the beacon just before the attack. The doctor describes him as 'always a bit unstable', but maybe this is what happens to a 'lesser mind' (as Liara put it).
  • The song that plays every time you die is Saren's theme song. Shepard was the only one that could stop Saren. Now they're dead and the Game Over music is Saren gloating.
    • The menu music is Vigil's theme.
    • The Citadel Tower theme is a near inversion of Sovereign's theme, only having more notes in its measure and being played with strings instead of brass.
  • The only time you hear two elcor speaking directly to each other is in the elcor ambassador's office. Careful listeners will notice they do not preface their conversation with their emotions. Of course, this is because they can detect the minor physical and pheromone changes of each other, and have no need to express them verbally.
  • A lot of lampshading is done by various squadmates about how "untrained civilians with makeshift defenses" on Feros held out for so long against a geth onslaught. At first glance, it would reinforce that Humans Are Warriors, until you ask yourself how the same species of tenacious fighters crumbled so easily on Mindoir, Eden Prime and X57 near Terra Nova to similar enemy assaults? Only later do you realize that these colonists were under Thorian control, and it was coordinating their actions to make any resistance meaningful. It was probably even reinforcing them with creepers and Shiala clones whenever necessary. Assuming they survive, their telepathic coordination comes in handy for ''3'' when they're fighting the Reapers.
  • If Shepard chooses to chat to the Council after Feros and picks the Paragon options, the salarian councilor reminds them that sacrifices will have to be made at some point. He probably wasn't expecting that Shepard can choose to do exactly that to him and his fellow councilors during the final battle.
  • Being forced to choose between saving Ashley and Kaidan, which forces Shepard to have at least one non-human squadmate before Ilos. This decision reinforces that even a renegade Shepard needs non-human help to succeed. “Humanity first doesn’t mean humanity alone” indeed.
  • Sovereign refers to the Citadel and the mass relays as "the legacy of my kind." It's not the legacy the Reapers left behind. It's the legacy they inherited.
  • The Colonist and Sole Survivor origin stories give you both paragon and renegade points to start with. Initially, this makes no sense; how is everyone around you dying related to your morality? Then you realize that the experiences were so traumatic that Shepard's psyche was partially fragmented. Also, those two backgrounds are morally neutral compared to Spacer/War Hero (Paragon) and Earthborn/Ruthless (Renegade). Colonist Shepard was raised by loving parents (Paragon), but probably had to do some dirty things to survive (Renegade). A Sole Survivor Shepard likely tried to help the other marines (Paragon), but eventually gave up and focused on self-preservation (Renegade).
  • In the final mission, Saren is marching into the Council chambers and takes a potshot at one of the Keepers maintaining the station. He did that because Sovereign was frustrated that the Keepers had not functioned as they were designed to and was taking it out on them via Saren.
  • Your squadmates each represent one of the classes: Ashley is a Soldier (all combat), Garrus is an Infiltrator (combat/tech), Kaidan is a Sentinel (tech/biotic), Liara is an Adept (all biotic), Tali is an Engineer (all tech), and Wrex is a Vanguard (combat/biotic). There are some differences, but the basics are there. Further, the only squadmates whose skills are identical to Shepard's are Ashley and Kaidan, because they too got their training from the Alliance. Everyone else's training is slightly different, and for good reason:
    • Garrus and Wrex are trained in Assault Rifles, which are normally only available to a Shepard who is a Soldier. This is because in both of their societies, they were trained as soldiers. Without this training, Assault Rifles would be near-useless to any Shepard besides a Soldier. This way, you can at least hand them off to a squadmate.
    • Garrus gets Adrenaline Rush instead of Immunity, which makes him more of a Glass Cannon than Infiltrator Shepard but allows him to spam tech and weapon skills (i.e. Assassination) much faster.
    • Wrex is a tank on two feet, so naturally he has access to both Immunity and Barrier but not Adrenaline Rush like a Vanguard Shepard would have.
    • Tali can use shotguns because of her military training on the flotilla (which would favor close-quarters combat and having to fight through ship corridors). But because she's a starship mechanic and not a doctor, she doesn't get the Medicine skill that a Engineer Shepard has.
    • Liara is the only squadmate with no military training at all, so she doesn't have access to any weapon skills (Adept Shepard at least has pistol training). The Electronics skill she has instead is hints towards her future occupation as the Shadow Broker. This skill also ties to the fact that she's a scientist/archeologist; spending almost fifty years on remote dig sites deciphering complex Prothean artifacts helped too.
  • In Retribution, when Grayson is resisting against the Reapers' control, they subtly shift his thought processes to make him decide to find Kahlee, which is what the Reapers want. When Shepard and Saren meet on Virmire, Shepard begins to instill doubts in Saren's mind about Soverign's indoctrination, before Saren suddenly turns angry and declares that his plan will save countless lives before attacking Shepard to prevent them undoing his work. Sovereign was doing the same thing to Saren that the Reapers did to Grayson; subtly shifting his thought processes to make him attack instead of stopping to listen.
  • Everything Jenkins says before Eden Prime foreshadows the upcoming events. He says that if a Spectre goes rogue, the Council will send another Spectre to deal with him. Chakwas dismisses this as romantic fantasy from a naive kid who watches too many vids, but Jenkins was right: Saren goes rogue and Shepard is sent to take him down.
  • The Citadel Fleet and the Alliance 5th Fleet are completely outmatched against Sovereign. A key detail that is easy to miss though: Sovereign was a full-up dreadnought (and a very powerful one at that), while the Citadel and Alliance ships (save for the Destiny Ascension, which was not fighting under the conditions she was built for: Long range slugfests) were cruisers or smaller. Of course Sovereign has the upper hand, especially if the Alliance was also having to deal with the geth ships.
  • Sovereign is a sovereign derived from a social contract made by its constituent intelligences, as detailed in Jean-Jacques Rousseau's The Social Contract.
  • The romances with Ashley and Kaidan seem very reserved before Udina grounds the Normandy and the crew heads to Ilos. There's plenty of flirting and questions about the relationship, but no physical affection. Why? Alliance regulations. Shepard is Ashley/Kaidan's commanding officer and getting involved with your subordinates while on a mission is a huge military no-no. They can talk about what to do when the mission is finished, but are holding back for now due to protocol. It is only after the Council screws Shepard over and the team is willing to sacrifice everything to go after Saren that Shepard and their love interest essentially decide that they will not get another chance and take things to the next level. With Ashley, add to it that Shepard is an officer and Ash is a noncom. Enlisted/officer relationships are equally frowned-upon.
  • At first, Saren's plan seems illogical. A Spectre, someone with virtually unlimited authority, could just walk right into Eden Prime, use the beacon, and then sabotage it to frame the humans. Instead, he grabs both the Villain Ball and the Idiot Ball, organizing a massive geth assault and revealing Sovereign. While it would have been deemed a wholly geth assault had the Normandy, Nihlus and Shepard not been around, it makes sense when you factor in that it's Sovereign's plan, not Saren's. Sovereign doesn't care one bit about Saren's Spectre connections or being subtle (and with good reason, as he's possibly facing a You Have Failed Me from Harbinger for screwing up so many times to open the Citadel relay), and they would actually benefit from getting the organics' attention. With the forces of the Citadel spread thin guarding against another geth attack, Sovereign could more easily break through the Citadel. Also, since Saren is trying to resist Sovereign's indoctrination, it's quite possible he's being illogical on purpose, hoping that someone will discover his plot and stop him. Even if Sovereign succeeded, Saren's movements would help the council races get a good and clear look at Sovereign.
    • Similarly, cloning the rachni, curing the genophage, and making the connection between the Thorian and the Protheans seems like too much of a Deus ex Machina to be real, until you realize that a "machine god" (Deux Ex Machina translates to "a god from a machine") did indeed do all of these things: Sovereign!
  • When the Citadel Council (still mistakenly believing the Conduit to be the entry point for any invasion rather than the Citadel itself) decides to deploy fleets to guard every relay between the Citadel and the Mu Relay, they are caught off-guard by Sovereign and the geth fleet, which completely bypass these lines of defense. How Sovereign was able to do this seems unclear until the Arrival DLC of 2: the Alpha Relay. This relay has hidden capabilities that allow it to send ships to any other relay over half of the network. And since it's in batarian space, nobody allied with the Citadel would have known about it.
    • It was never a mystery, they explicitly used the Conduit to reach the Citadel. The Conduit was an entry point for an invasion, but for the Geth rather than the Reapers. The Conduit was the mass-relay the Protheans built on Ilos that leads directly to the Citadel, and the one Shepard uses to get back there in time.
  • All the collection quests may seem like nothing but an annoying way to gain experience, but when viewed from a paragon point of view, they can also be interpreted as Shepard trying to further humanity's relationship with the council:
    • Asari Writings improves relationships with the Asari, because you are collecting a long-lost part of their cultural and literary heritage.
    • Turian Insignia does the same for Turians, thus improving relationships with them.
    • Signs of Battle has you collect medaillons that belonged to a Salarian Shadow Organization disbanded upon discovery of the Citadel. The operatives were never apprehended, so you are essentially finishing the Salarians' job for them.
    • Prothean Data Disks and Minerals are valuable to every species, thus improving relationships with every one.
  • In a case of both Fridge Brilliance and Fridge Horror: If Wrex is killed on Virmire, you will get all his equipment back as if it were ordinary enemy loot.
  • All armor is race specific except for the asari. There is no asari specific armor, likely because asari can tune the nervous systems to that of any other race and can hence adapt to their armor. More specifically, asari are the only race who are the same shape as a human female, with no other biological factors to consider when making armor. Even a quarian (the next closest species) wouldn't have the same number of digits on their hands and feet, so they'd need their armor to be at least partially customized.
  • Benezia doesn't fight like her commandos. While the commandos move very nimbly, use warp and throw at range before closing in to finish you off with shotguns, Benezia can only use Throw and Stasis, stands in one place and fires at you with an assault rifle. Why this discrepancy? Because Benezia never went through the huntress training that her commandos went through. Stasis and throw are defensive powers, befitting a typical noncombatant asari.
  • Why are the Normandy's emissions blue shifted when she jumps to FTL instead of red shifted? Because of relativity. At subluminal speeds, the light from your destination always reaches an observer after the light from your source. Because the observer perceives light from farther and farther away, it appears to red shift to lower frequencies. At superluminal speeds, however, things work backwards. Because you are moving faster than light, the light or EM radiation from your destination reaches an observer before the light from your source. They would perceive you as coming towards rather than going away. Your emissions therefore increase in frequency, hence the blue shifting.
    • Why does this give away the Normandy's position? Because everything in-universe is normally red shifted (owing to the Big Bang), so a sudden speck of blue radiation would stand out. An observer would see this for any ship transiting systems via FTL, but you rarely, if at all, find patrols in between systems.
  • Benezia reports to Saren after Eden Prime that the colony was destroyed as Saren had ordered, but one of the humans from the Normandy might have used the beacon. As Saren files into an Unstoppable Rage, the lighting in the room pulses a very angry red...which then snaps back to stark blue when Saren shifts to Tranquil Fury. This is Foreshadowing the truth about Saren's "flagship" before the Reapers were ever introduced.
  • Why are all crew members so willing to follow Shepard and ignore even their most evil deeds? All of them lost their fathers under tragic circumstances, and Shepard, a charismatic leader, might have become their Parental Substitute. Wrex murdered his militarist dad and was exiled for being too liberal for Krogan, and then he encounters someone willing to end all wars; Liara has never met Aethyta and was raised by a strict mother; Ashley grew up in patriarchal family with father guiding and supporting her until he passed away; Garrus' father was a military man, a bureaucrat and a real Turian who always mistreated his son for his rebellious nature; Tali's dad neglected her and her talents; and Kaidan was forcefully separated from his father as a child.
  • At the end of the Cornucopia mission, it's surmised that the crew found a strange artifact that indoctrinated them and made them fly into the Perseus Veil where the Geth reside, then came back with husks as a "warning" to others not to go into the Veil. Knowing that the Reapers are not allies of the True Geth, it becomes clear it was a False Flag Operation by Sovereign and the Heretics to keep people from contacting the True Geth.

    Fridge Horror 
  • When you're at the Peak 15 research labs, you can trigger the neutron purge early and wipe out the Rachni. If you do this, when you come back you'll find Captain Ventralis and his mercenaries, who tell you that they've got new orders from Benezia, and start shooting. He even apologizes about having to do it, too. After wiping them out, if you look around, you'll find all the scientists and workers are gone. All of them. Everywhere. And there's nowhere for them to have gone... which leads to the rather frightening yet logical conclusion: Ventralis and his men didn't just have orders to kill you, they were ordered to wipe out everyone at the research station. Confirmed when you talk to Han Olar (the traumatized volus scientist) after saving him from Benezia's forces.
  • Luna VI:
    • That "Rogue VI" on Luna that you destroy was actually EDI before she was augmented with Reaper tech. The same EDI who is standing right next to you when this is revealed. Good thing she doesn't seem to hold a grudge about it. This gets further awkward when revisiting the beginning of Mass Effect 2: when EDI appears the Renegade option is to act hostile towards her, which prompts Miranda to point out to EDI that Shepard has had bad experiences with AIs... and brings up the Luna VI (aka EDI) as an example.
    • It's very easy to overlook, but if you read up on the information regarding the "Rogue VI", you'll find that someone DELIBERATELY tampered with it to cause it to go crazy. There's no investigation as to who exactly did it, but in Mass Effect, there's a short sentence mentioning how there were signs of tampering with it's controls before it started killing people. When you think about the above point from Mass Effect 2, it was nowhere stated that the Luna VI was an AI, yet Miranda directly refers to it as one. How could she have known if it was an AI? Easy: she's working for Cerberus, who tampered with the VI to make it an AI.
    • On the subject of the Rogue VI on Luna, after you defeat it you get a popup explaining that Shepard's comm gets filled with white noise that was converted to binary. If you then further convert this binary into ASCII, it spells out the word "HELP". Especially horrifying if it was an AI as the above theory posits; it was sentient, it asked for help, for mercy... but you killed it anyway.
  • After Saren shoots and kills Nihlus, we see him brooding in his chair and looking pretty sullen before he learns that Shepard thwarted his attack — so he was acting pretty broody even though he thought he'd succeeded. He seemed pretty much a sociopath when he killed Nihlus, and he starts chucking things around in an obvious tantrum, and yet for the rest of the game he seems to be a pretty calm, if determined person, right up until the end when he shoots that keeper. So that seemed a little strangely out of character. Later on, we see that when he's indoctrinated, his eyes glow blue, and they stop glowing when he fights it. Replay the game, get to the scene where he meets Nihlus, and you'll see that his eyes glow blue when he shoots Nihlus. It especially further explains why he sounds desperate and even a bit pleading when he talks about researching and fighting indoctrination.
  • A bit of Fridge Sadness. More than once, there are hints that Ashley and Kaidan were attracted to each other, especially if Shepard is romancing Liara instead. Obviously, this is a doomed ship. On Virmire they were both telling you to save the other one. They weren't just being heroic - they were trying to save the person they loved (or, at least, had feelings for)!
  • Buried away in the Codex is the fact that the genophage does NOT affect krogan fertility rates - it affects fetal viability instead. The previously-fecund krogan aren't simply subject to low birth rates - they are subject to entire litters of stillborn babies.
  • Why does Saren/Sovereign want to send the geth to kill off the Thorian even after getting the Cipher from it? After all, the Alliance could have remained in the dark about their dealings with the Thorian had it not been for the geth onslaught that followed. They could have used the Cipher to find the conduit covertly with none being the wiser. Until you realize that the Thorian is a sentient organic species capable of undoing indoctrination, enthralling other organics and hibernating for over 100000 years - this thing can easily sleep through multiple reaper harvests and then use its thralls to act against them later. It could even become a new Leviathan equivalent.
  • Several assignments can become just this when you think about them for a little longer:
    • The MS Worthington is completely empty except for brain-dead Jacob and his psychotic biotic girlfriend Julia, meaning that sometime between killing the captain and Shepard's arrival Julia killed the entire crew. Why did Julia flip out like that when her boyfriend was placed on futile life support? She most likely was an L2 suffering from mental instability due to her implant. That ship had a ticking time bomb kept in check only through The Power of Love. (Edit by other author: If you read/listen to the logs you learn that she attacked the others on the ship because they were going to turn his life support off, and let him die naturally, a choice that Shepard has the option to make. The logs also state that he was one of the few helping her maintain her sanity, although I can't remember if it states if her implant was an L2.)
    • The missing survey team on Trebin were all converted into husks and - according to a data log - had previously discovered an alien artifact that turned them into mindless machine worshipers. When you enter the mine where you find the survey team, you realize that the only alien artifact in the room is this glowing orb inside a mechanical claw that looks just like the "geth temple" on Feros and remarkably similar to Reaper Tech. Which means that: 1) the survey team became indoctrinated and essentially huskified itself, and 2) the geth on Feros may have been indoctrinated as well, instead of being willing worshipers. What makes this even worse is that Shepard and his crew say that they have heard about such devices/artifacts before, meaning indoctrination has been around a lot longer than believed.
  • At first the company spokesperson on Feros, Ethan Jeong, seems rather cheesy and 2-dimensional with how much he blatantly obsesses about company profits over of the lives of the colonists, until you realize that, by this point in time in galactic history, corporations have become so powerful that they barely need to hide their greed anymore. Jeong is an example of the arrogance corporations have now that they can own entire planets (e.g., Noveria), and don't even need any sort of a human face when dealing with colonists in the Traverse that nobody cares about. (If anyone in the galaxy did care about the colonists, Shepard presumably would not have been necessary to drive out the geth.)  
  • If you start a fire fight in the wards markets during one of the assignments, all the shop owners will immediately duck. As soon as the fight is done, they will stand up again and immediately continue treating you as if nothing had happened. These guys are civilians, but apparently nearly getting shot while on the job is just Tuesday for them. Makes you wonder what else happens down there...
  • On Noveria at Rift Station, you learn about a bioweapon called Thoros-B, that broke out of containment and infected a few researchers. It is in fact a quest to “mix” the cure. Dr. Cohen the project lead for this bioweapon and the quest giver claims that this contagion was intended initially to “kill a creature encountered on the frontier” and that they didn’t want it to infect anyone other than its target - a “biowar attack without a pandemic spread” in Cohen’s own words. When you get to the quarantined lab to mix the cure, and if you haven’t done the Missing Recon team quest yet, the codex for Thresher Maws can be unlocked in that lab. Conclusion - this bioweapon was made strong enough to kill a freaking thresher maw and it’s virulency was neutralized because they didn’t want a thresher maw killer infecting colonists. So, those people moaning and groaning in Cohen’s lab were dying from something intended to kill thresher maws.

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