Action Prologue: Razor's Edge begins with the Collector attack on the Normandy, same as Mass Effect 2.
Adaptation Distillation: In the first story, the events of Zaeed's and Kasumi's loyalty missions are combined into one chapter, with Vido Santiago and a bunch of his Blue Suns thugs being guests at Donovan Hock's party and an explosion in the vault causing the fire that threatens to kill a lot of civilians.
Similarly, Samara and Thane's recruitment missions are combined.
On another note, the events of the Overlord DLC are not touched upon at all, probably because the author hadn't played it when he started writing the series. The Arrival DLC isn't really dealt with in much detail, but that's because the author does not like that particular DLC at all and has expressed irritation at how heavy-handed the plot's Railroading is in it.
Also, perhaps more in the vein of a Pragmatic Adaptation, some of the more humorous elements of the Mass Effect universe that are Leaning on the Fourth Wall are absent: examples include Conrad Verner and the Friend Zone Turian/Valley Girl Quarian, who are nowhere to be found in this series.
Adaptation Expansion: Many events in the games that seem improbable or outright silly are given serious consideration as to how they could have happened. A very notable example is the Cerberus takeover of the Citadel in Requiem. Considerable attention is paid to how exactly an N.G.O. Superpower would be able to invade a space station that is 25 kilometers long and defended by a powerful multinational fleet as well as how difficult it would be to repel an invasion of that magnitude once it had become firmly entrenched.
Arch-Enemy: Razor's Edge treats Saren as Shepard's most personal foe.
Armor-Piercing Question: Ghost!Saren give Shepard a rather awesome one while he is suffering from the Reaper's attempt at indoctrination on Rannoch. "Then why are you the one running?"
Ascended Extra: Kasumi is one of the major characters in this fic. She gets a lot more screen time compared to Canon, is best friends with Tali, and in Requiem even rejoins Shepard. Also has a great deal of Ship Tease with Garrus.
Also the Rachni have a FAR larger part during Requiem than in the canon game.
Considering that she was nothing more than a very minor, unnamed sidequest character in the second game, everything about Quin'Sala a.k.a. Slave Girl Quarian on Ilium. She's appeared in every Razor's Edge installment.
Lia'Vael nar Ulnay also gets a little more screen time in the first story by getting to share some girl talk with Tali. Then she gets into some troublesome shenanigans with Kolyat in Dark Witness.
Miranda Lawson has a much larger role in Requiem than in the vanilla Mass Effect 3, with Shepard hand-picking her to lead the operation to liberate Omega from Oleg Petrovsky.
The Atoner: Han'Gerrel after the events of Rannoch.
Awesome, but Impractical: Shortly before the battle of Rannoch, Kasumi enlists the aid of Legion and the rachni to upgrade Shepard, Garrus, and Tali's armor with miniaturized quantum entanglement communications devices. Shepard is the first to ask if it would be possible to distribute these across the entire war effort. Legion's answer is no, since a single one of the devices costs the equivalent of 168.3 million credits. Or enough to build an entire frigate.
Awesome Moment of Crowning: After a plan is made to officially unite the galaxy under a single banner, an Alliance devoted to destroying the Reapers, the Commander is unanimously voted by all the races into "Praetor" Shepard.
Also Shepard versus all his fears and the Reaper's powers in the form of Saren. Shepard wins.
Berserk Button: Don't threaten Shepard's crew. Just don't. Anderson sums it up nicely:
James Vega: "(Anderson) told me personally that under no circumstances were any threats to be made against any crew that remained aboard and if we did it would only end badly for all of us. Said that went double if (Garrus was) still aboard and that 'god help your stupid grunt soul if the quarian on the crew manifest gets caught in the line of fire'."
Beta Couple: Oddly enough, in Requiem Shepard and Tali could be considered the Beta Couple for Garrus and Kasumi.
Garrus: "Sooo... You forgot to mention the AI, huh?"
Tali: "The WHAT?"
Black and Grey Morality: In Razor's Edge, before going through the Omega-4 Relay, Shepard knows the Normandy needs to be upgraded. Unfortunately, there are no ports where they can do so... except for Omega, which means he needs to get on Aria's good side. Said deal consists of taking along Garrus and Legion to form a team of Cold Snipers and eliminate an upstart drug-smuggling group that is growing too quickly for Aria's liking. Essentially, Shepard and friends end up contracting themselves out as hitmen in a petty gang war. Things get worse when it turns out that some of the drug smugglers they've been contracted to kill were enslaved teens and preteens, which really pushes Shepard's Berserk Button...
Blessed with Suck: Shepard's biotic abilities during Razor's Edge. Since he hasn't had any training he can't use them without getting crippling headaches. This is mostly averted by Dark Witness due to training from Jack. By the time Requiem rolls around Shepard has had 6 months to practice and can fling biotics with the best of them.
Bottled Heroic Resolve: Thane has one created with a medicine designed to artificially increase the oxygen in his blood combined with several highly illegal stimulants, it allows him to race to the Citadel tower, take out several Cerberus agents along the way, and stall Kai Leng long enough for reinforcements to arrive. The side effects from the drug are pretty severe but Thane dies before they become an issue.
The Brute: Kai Leng, whom The Illusive Man considers to be little more than a rabid attack dog.
Call Forward: EDI notes that the windows in Shepard's cabin are equipped with armored shutters so they won't be structural weaknesses.
Casual Danger Dialogue: All over the place from Shepard and Garrus but Tali and Hanah Shepard have a great moment in Dark Witness, discussing Shepard's stubbornness while hunkered down behind a table exchanging shots with some thugs.
There's also this exchange when Shepard (wearing armor Liara got him) is being thrown around the battlefield by a brute:
Liara: "Shepard! Get out of there!"
Shepard: "I've got nowhere to go, Liara. Armor is good, though. Thanks."
Chronic Hero Syndrome: Shepard, oh so much. Just about everyone comments on how he's unable to stop trying to solve other people's problems.
Coitus Interruptus: A running gag in the aptly named chapter "Interruptions" is Shepard and Tali getting interrupted just before they get started.
Cold-Blooded Torture: Shepard just threatens an assassin with this to get him to talk, but he was perfectly capable of carrying out his threat.
Cowboy Cop: Bailey, more so than in canon. He captures a group of assassins that he doesn't have the authority to arrest, and even if he did, they'd be out in a few days. So, he looks the other way as Thane kills them all.
Dead Man Writing: Mordin leaves a message to be seen by Shepard after his death.
Death by Adaptation: While Anyone Can Die in the Mass Effect ganes, one very notable death in this fic is Miranda killing Aria after it is clear she will not allow anyone to stop her from murdering Petrovsky after his surrender. Notable because this is one of the few major characters in the games that cannot die outside of the "Refuse" ending.
Defiant to the End: Shepard's response after being cornered by Rachni husks while the Reapers make one last attempt at indoctrinating him? Pull out a couple of grenades.
Demoted to Extra: Many of the new characters introduced in Mass Effect 3 suffer this fate in Requiem, such as Cortez, Traynor, and Vega. Even Javik hasn't done much after being recruited.
Didn't See That Coming: Shepard's newly developed biotic abilities end up being a lifesaver twice in Dark Witness since no one knows about them.
Dirty Business: Shepard feels this way about destroying Purgatory, and makes sure that the responsibility is his alone.
Shepard also considers his choice to work with Aria and kill a convoy of drug dealers this.
Disappeared Dad: Shepard's dad was on Mindoir when the Batarians attacked it.
Drives Like Crazy: Detective Anaya. It doesn't help that her 3-seater car is carrying five, either.
Drowning My Sorrows: Shepard has a couple episodes of this early on in Razor's Edge. He eventually gets better.
Empowered Badass Normal: Shepard becomes a biotic as part of the Lazarus project. Said project also stuffs a great deal of cybernetics into him, making him considerably more durable and strong than a typical human.
Everyone Can See It: Shepard and Tali's feelings for each other were apparently the worst kept secret on the Normandy in Razor's Edge, to the point that most of the ground team as well as Joker and Chakwas had a bet on when Shepard and Tali would publicly admit their feelings for each other.
Fantastic Racism: Kai Leng as in canon, but the segments from Leng's point of view really take the cake. He even refers to Shepard and Tali's relationship as being "No better than bestiality."
Flashback Nightmare: Shepard has one while he's being revived by the Lazarus project which starts like this, with him reliving Akuze. Then his current squad takes the place of his old one...
Fire-Forged Friends: Fighting off a squad of assassins together addresses all of Hannah Shepard's concerns with Tali dating John Shepard.
Four-Star Badass: From Dark Witness, Rear Admiral Hannah Shepard of the Orizaba.
Aethyta: "Real dark liquor and an equally dark beer, I think there might even be some other minor shit in there. Apparently named after a plague on their world. They say every third one kills you."
Genre Savvy: Anderson is well aware that harming Shepard's crew is a BAD idea. When Vega and a group of marines were going to take Shepard into custody Anderson personally told Vega that any threats against the crew would go badly, that it went double for Garrus, and that 'god help your stupid grunt soul if the quarian on that crew manifest gets caught in the line of fire.'
Head-Tiltingly Kinky: When Shepard's team watches Fleet and Flotilla, the... interactions between the stars are never described, but plenty can be inferred from the reactions of the viewers.
Heel-Face Turn: Quite unexpectedly in Requiem, the ghost of Saren undergoes a dramatic change after Shepard rejects his existence as a Reaper puppet. Unlike most examples of this trope, though, he does not become purely helpful, but rather goes from being outright antagonistic to simply being pessimistic about their chances of success.
Heroic BSOD: Shepard goes into one when facing the Thresher Maw on Tuchanka during Grunt's rite. Shepard also has a big one earlier after confronting Liara on Illium.
Heroic RROD: Thane takes a drug to re-oxygenate his blood and allow him to function at his peak for a short time, but it will severely worsen his already critical condition once it wears off.
Heroic Willpower: Part of what allows Shepard to resist Reaper indoctrination. As for the other part...
The Reapers' ability to warp the mind found root in the doubts and fears that lived in the psyche of every man, woman, and child. To purge him of that influence would have been to purge what made him human, to make him like the workers and soldiers of rachni, one mind among the whole without fear or doubt. Hope-Singer's song couldn't banish the twisted call of the Reapers, but it let him see it for what it was.
He's Back: Shepard, after Utukku. And an awesome comeback it is!
Hurting Hero: Shepard. In addition to the very hard choices and grinding losses of canon, he also has to deal with being indoctrinated, which does a number on his mental health. As the story goes on it becomes a race to defeat the Reapers before Shepard falls apart.
Meaningful Name: All the names given by the Rachni. According to them it isn't so much giving a name as "We sing only of what we see within."
The Rachni queen: Hope-Singer
The Turians: Predator-Singers
The Krogan: Survival-Singers
The Asari: Long-Singers
The Salarians: Singers-of-Bright-Brief-Songs
The Quarians: Wander-Singers
The Reapers: Dark-Song Destroyers
Synthetics in general: Cold-Singers
The Rachni can't even give a name to Kai Leng's song.
Banshees don't sing. They scream.
Memetic Badass: Referenced In-Universe in Requiem when after Shepard's return from the dead Wrex mentions that "One of our younger warriors said that krogan might have two hearts, but no krogan can ever claim to have had three lives."
Moment Killer: In Razor's Edge a moment between Shepard and Tali is interrupted by the Collector attack on the Normandy. In Dark Witness Tali and Shepard are interrupted multiple times to the point that its almost a Running Gag.
Morality Chain: Tali is the reason Shepard is still sane. This fact is readily acknowledged by Shepard and The Illusive Man.
Mythology Gag: The bomb that explodes on the Citadel and critically injures Kasumi is pretty much how she dies in Mass Effect 3 if she is not loyal while doing the hanar ambassador sidequest.
Noodle Incident: Everything that occurred during the events of Mass Effect 1, as lampshaded in Requiem when Vega presses Garrus for more details. In particular, though, is an event referenced by Tali in Razor's Edge she calls the "Tartarus incident" when Shepard lost his cool against a gang of pirates who were apparently torturing kidnapped colonist children. The fact that the pirates then threatened to rape and kill Tali really pushed Shepard over the edge. It should be noted that the incident in question is nowhere to be found in the game (there aren't even any locations called Tartarus in Mass Effect 1).
Not What It Looks Like: The video file the Shadow Broker sends to Tali is designed to cast Shepard in the worst possible light.
Not So Different: Shepard's cybernetics, Renegade tendencies, Spectre status and indoctrination remind him of Saren.
One Head Taller: Garrus is a good foot taller than Kasumi, with whom he frequently trades banter and eventually romances.
Our Hero Is Dead: The Utukku mission when Shepard seemingly blows himself up to fight off both indoctrination and Reaper-controlled rachni. True to the trope, the rest of the crew is convinced he's dead and flees. One chapter later, he's alive.
Poor Communication Kills: The Shadow Broker's attempt to turn Tali over to his side in Dark Witness could have been alleviated if Shepard had talked to his girlfriend a bit more after noticing she seemed sullen at having Liara on board again.
Ditto in Requiem: Shepard's deteriorating mental state might not have gotten so bad if he'd been willing to come clean about his indoctrination and his freaky dreams to somebody, anybody. Given a Lampshade Hanging right before he performs his Heroic Sacrifice. Though he survives.
Shoot the Dog: For most of Razor's Edge, Shepard is more or less a pretty straight-up Paragon fellow. Thus, it comes as a pretty strong shock when he allows Maelon to leave the Weyrloc compound, only to then climb up to a 2nd story window and coldly shoot him In the Back at a hundred paces. A stark reminder that this Shepard is an Infiltrator who has done his fair share of dirty work in his career. And earlier he blew up Purgatory.
There's also his killing of Donovan Hock, because no cop could touch him if Shepard just arrested him.
In Requiem, he seriously contemplates killing Mordin on Tuchanka. Even Garrus is unsettled by this.
At Hock's party, Kasumi changes a password to Dagobah.
The entire sequence of Shepard clawing his way out of the caves of Utukku is one long shout out to Bruce Wayne's rise from the Pit in The Dark Knight Rises. According to comments by the author from the talizorah.org fansite, the scene had been planned out well in advance of the movie's release, but after watching the film, he couldn't resist making it more similar.
Fun fact: the author didn't actually know about it at all.
Something Only They Would Say: Just like in the game, Shepard convinces Tali that he's really alive by reminding her of the Geth data he gave her. In this case, the scene is made much darker as the nearly hysterical Tali is fully prepared to blow the brains out of who she believes is an imposter.
Come Requiem, and Mordin precedes to blow this trope to hell and back with three simple words "Do not ingest."
Spit Take: Happens to Shepard twice during Dark Witness. The first is when Garrus invokes it by waiting for Shepard to get a glass of water before mentioning that the Orizaba, the ship his mother commands, will be at the Citadel soon. The second is when Hannah Shepard mentions that due to the incident of some thugs nearly killing her and Tali, she can skip straight to asking Shepard awkward questions about his sex life (right when he has a cup of hot coffee). Shepard Lampshades that he really needs to keep liquids away from himself when others are talking to him.
Tali: "You're just being nice because I'm on to your plan to lure me back to fix your engines so you don't have to get dirty.
Shepard: "With all the upgrades we're talking about, chances are I'll be down there helping you, so my cunning plan must not be working too well. Besides, if I'm going to get dirty, I figure might as well be with a friend. That... came out sounding very different than it did in my head. Let's just pretend I didn't say that."
Took a Level in Badass: Quin'Sala, the quarian Shepard rescues from indentured servitude in Razor's Edge, learns how to handle a shotgun from Matriarch Aethyta. By Requiem, she helps repel the Cerberus assault on the Citadel.
Tranquil Fury: Pretty much the entire team after the crew of the Normandy is kidnapped by the Collectors. Shepard in Dark Witness after some thugs start shooting at Tali and Shepard's mom and when the Shadow Broker nearly kills Tali. In all three cases large amounts of ass-kicking follows.
Undying Loyalty: The Shadow Broker notes that Shepard inspires this in people, as evidenced when he tried to contact members of the Normandy's crew and pay them off to sell out their boss. In particular, the Broker was quite surprised to see that even ZaeedMassani refused to betray Shepard for credits.
Villainous Breakdown: Averted compared to canon with the Shadow Broker. The fact that he still has one more card to play probably has something to do with it.
That card is implied to be the only reason this trope is averted however, and sure enough, once it's revealed that Tali double-crossed him, the Shadow Broker proceeds to play this trope straight.
Wham Episode: Requiem has the side-mission on Utukku take an unexpected turn when it appears that Shepard has sacrified himself to save the Rachni and destroy the Reaper forces!
What the Hell, Hero?: Garrus reads Shepard the riot act after the Tuchanka missions, where Shepard nearly decides to kill Mordin, and didn't fill Garrus in until afterwards. Shepard justifies his actions as I Did What I Had to Do.