Ain't No Rule: While Hackett admits the idea of putting a revived Master Chief forward as a Spectre candidate is ridiculous on paper (in a manner of speaking), he immediately and eagerly Hand Waves the issue by citing this trope. The Chief hasn't even been thawed by the time he gets behind the idea.
Standard for Mass Effect, but N'tho takes it to a whole new level, him being a "Squidhead," someone who appreciates human culture. He loves human poetry, songs, and books.
On a more species-wide scale, according to N'tho, after the Human-Covenant war, the entire sangheli species fell in love with burritos. Apparently, their tube shape is perfect for the oddly-shaped mouths of the sangheli.
Arc Number: True to form, variants of the number seven appear throughout the story. For example, some of the "named" Geth troopers have serial numbers divisible by seven, and not counting the Chief himself, there are seven members of the Normandy ground team.
After the events of the above, Cortana decides to update her appearance with longer hair, a dress and the color pink, but the Chief is so dumbstruck by it that she said that she'll revert to her previous appearance when they're alone.
The Arbiter. Even for a species as long-lived as Sangheili, he admits he's in the Twilight of his life. However, he still singlehandedly assaults a mercenary compound, and even after reuniting with Chief and Garrus, continues to hold his own and sends enemies fleeing in terror.
Technically, the Chief counts as this as well, but Cryo-freezing has a lot to do with it. Even counting that, he's still pushing fifty.
Badass Normal: According to Tali, Kal'Reegar came back from his Pilgrimage with a suit full of injuries and a gravity hammer. His answer to the obvious question ("How did Kal'Reegar get it?") was simply, "It wasn't easy."
A meta example is the author launching into a rant over how he's angry the Jackals don't have their signature beaks in Halo4.
Blue and Orange Morality: A minor example, but Ashley is stunned when N'tho reveals that not only is one of his brothers the result of someone who isn't N'tho's father having slept with his mother, but that N'tho's father is proud to have let that Sangheli bed his wife. N'tho explains that the stranger was a swordsman, and that while they aren't allowed to be married, they are allowed to bed many females in order to pass on their swordsman genes. It's considered an honor to raise a swordsman child in Sangheli culture.
Bond One-Liner: Not even the Chief is immune to dropping these every once in a while.
Khalisah al-Jilani tries to paint the Chief as this after he blows off her interview. Hackett is displeased with both of them and warns Chief that the fight for Feros is going to have to be a vital PR boon for the Spartan.
Another minor example for Kaidan, where he views how the Chief is going to coldly execute biotic terrorists by pumping all the air out of their ship, where he's reminded that while the SPARTAN-II program did save the human race from the Covenant, at the same time they were originally for suppressing human rebellions against the UNSC.
But He Sounds Handsome: While under an alias, the Chief ends up arguing with Charles Saraccino, the head of the Terra Firma Party, over whether the Chief was justified in bringing non-humans aboard the Normandy.
He's also written several thesis papers about alien cultures, and is writing another on the Normandy comparing the writings of a famous asari matriarch with his own culture.
Casual Danger Monologue: N'tho talks to Tali about a rock n' roll variant of Rocky Road to Dublin and a lesson about the historical context behind it. Tali, however, is too busy clinging on for dear life as N'tho drives down a Prothean skyway teeming with geth and Krogan.
Character Development: Master Chief's suspicions about both the former Covenant and "new" races slowly but perceptibly erodes over the course of the story.
Chekhov's Gun: The Forerunner Relic the Asari Consort gives to the Master Chief turns out to be a key that lets The Spartan's team access The Registry two story arcs later.
The armor that Chief gained from an unknown benefactor hinted at the existence of other Spartans being active, a possibility reinforced by sightings of the Ghost of Elysium.
Co-Dragons: Miranda and Kai Leng to the Illusive Man.
The Chief spends much of his conversations with Nihlus sizing him up and figuring out the best ways to hypothetically kill him (or other Turians, for that matter) just in case.
Wrex. He always seems to have something for the occasion. Of particular note is a T-Pack custom-fitted for Krogan use... which comes in handy when the team boards the SSV Ontario to defuse the L2 hostage situation. He brought it as an afterthought.
Creator Provincialism: As a "Squidhead," N'tho is fascinated with human culture, though much of the knowledge he shares focuses on Irish culture specifically. The author, incidentally, has mentioned being Irish. Hmm...
Cut Off The Head And The Body Dies: Averted from a heroic standpoint. The Normandy and her crew, especially Chief's team, is perfectly capable of handling themselves if contact with the Chief is ever lost.
While the Master Chief is a good soldier, he's not Shepard. He's not Paragon, he's not Renegade. He doesn't know how to deal with people. In chapter 37, he openly admits that he feels that the Council made a massive mistake choosing him as a Spectre. In short, while he's completely awesome in many ways, the ability to rip out a charging Jirlhanae's spine doesn't necessarily translate well to being able to deal with politicians, or former enemies. Shepard (in the games) was able to walk that line- he knew the galaxy well. For Chief, it was just last week that the same unggoy that sells him his grenades with a half-off discount for saving the galaxy... was charging at him insanely, screaming oaths to his god with two plasma grenades primed, ready to sell his life to stop "the Demon."
The "Proud Warrior Race Guy" attitude is deconstructed as well. At least one member of the political party "Slip To The Future," says that they believe that the Kig-Yar (Jackals) will likely have the next council seat after the humans get a seat, instead of the Sangheli. While the Sangheli are prominent leaders and proud warriors (especially in the Halo Games proper), they focus a lot of their energy on their military... and don't place nearly enough on other pursuits. On the other hand, the Jackals, while weaker than the Sangheli, still have a military that is strong for its size, and a booming economy, which would be far more advantageous to the Council.
Further deconstructed when N'Tho mentions that part of what the Sangheili had to re-learn after breaking from the Covenant was agriculture, plumbing and building and maintaining infrastructure and how they were so focused on being the Proud Warrior Race that their society was essentially non-functional without the Unggoy and other species supporting their society.
Defrosting Ice Queen: Master Chief to the Normandy crew, before his Kick the Dog moments start coming and then he freezes solid again. He starts thawing out again after a bit of soul-searching.
Degraded Boss: Cortana lampshades how fighting Geth juggernauts used to be hard.
Nihlus: Not the most glamorous assignment I've ever had. But no less important than any other I've been given. Besides, I've learned a long time ago that you never know when a boring assignment might turn interesting.
Drives Like Crazy: The Chief. N'tho is a lesser example, but he still makes his passengers plead for their lives.
Droit du Seigneur: one of N'thos siblings was sired by a wandering swordsman; who are not allowed to marry but are instead expected to sow their oats far and wide. A rare example of everyone being on-board with the idea; it's a great honour to bear and/or raise a swordsman's child.
"I can categorically say no, the place did not explode." Chief, in chapter 31. the Forerunner facility self-destructs by sucking everything into slipspace, similar to the method used to destroy the Long Night of Solace supercarrier in Halo Reach. That, if anything, was an implosion, where it collapses in on itself.
And again when N'tho, Kaiden, and Chief are discussing Chief's love life (or lack thereof):
John: "Whatever happened to 'didn't want to pry into my personal life behind my back?'"
N'tho: "I'm not prying into your personal life behind your back, I'm doing it right in front of you."
When Jondam Bau requests the aid of the Arbiter, he specifies that they should only take one ship to search for Halo. The Arbiter responds by indeed only taking one ship. The type of ship, however, is the same class of supercarrier that was used in Halo: Reach, namely, a twenty-seven kilometer long supercarrier which has enough soldiers and firepower to subjugate an entire planet.
Ashley and Jenkins towards the Master Chief, his historic influence being part of their inspiration to join the Alliance military.
The Biotic Terrorist Leader immediately surrenders after seeing the Master Chief in person, he and his followers having seen him as a hero as well. It helps that at Kaidan's suggestion, Chief attempted to negotiate with them instead of depressurizing their ship and suffocating them as initially planned.
Fantastic Slur: The former Covenant races regard their old nicknames as this and it's considered politically incorrect to refer to them as such. "Squidhead" doubles as N-Word Privileges for young elites.
Foreshadowing: After destroying a geth transmitter in the tunnels under Zhu's Hope, Wrex discovers that the three Krogan they killed to get to it were all adolescents, something he points out to the Chief is very unlikely.
For Want of a Nail: Because the Monster of Torfan killed all the Batarians long before his unit showed up, Major Kyle was never traumatized by the loss of his men, and never became a cult leader.
In Spite of a Nail: Instead, he becomes a catholic priest and winds up being called "Father Kyle" anyway.
The Councilors, however, admit to having been briefed on Halo's true purpose shortly after First Contact and take it seriously enough to send a Spectre looking for it once The Chief discovers Saren wants it.
Genre Savvy - Mixes with Combat Pragmatist, Ustrina the AI pulls out all the stops against Chief and his team, including: rigging omni-tools with deadman triggers to prevent hacking, installing cyanide gas tanks throughout the ship, cutting off the team's communications, and even simply holds off Cortana by choosing to erect powerful firewalls around her rather than face her directly.
Gilligan Cut: The Author loves to prove how wrong the characters are.
Good Counterpart: "Slip to the Future" is this for the Terra Firma party. It's an inclusive party comprised of many non-humans that nonetheless advocates Slipspace technology, an FTL technology (and humanity's primary method of FTL travel pre-Citadel) that the Council has banned. Mostly the same agenda, but none of the Fantastic Racism.
Grievous Harm with a Body: While fighting Geth inside the Therum excavation site, The Chief picks up a freshly killed Geth Juggernaut and starts running, using it as both a shield and battering ram to knock over other Geth.
Though just as emotionless as ever, the geth runtimes Cortana holds hostage and tries to interrogate remind her of her mortality as a smart AI made from flash-cloned brain tissue and her organic shortcomings. She's able to maintain her composure before destroying them, but it leaves her quite rattled.
In Chapter 30, Saren gives a caustic review of Master Chief's leadership skills, pointing out how many Marines died at his side despite seeing him as a Messianic Archetype and especially how a sizable number of Spartans died under his command. You'd think this would be suicide when it does work. Instead, Saren nearly Curb Stomps the Chief when he chooses blind rage over his normally clinical tactics.
The effect of the Hannibal Lecture is somewhat lessened when you've read enough of the EU to know that very few Spartans have died under the Chief's command. Most of them died under Fred's command.
Have I Mentioned That I Hate Synthetic Life Today: Ever since Cortana was revealed, Tali has been hit with this hard. Any attempt at Cortana trying to form any sort of bond with Tali is viewed with extreme suspicion, and she will frequently take any slight sign of betrayal as proof that the AI specifically designed to protect mankind, with a proven track record of doing so, is about to kill them all.
Hero of Another Story: The Arbiter has been investigating Cerberus for at least a month before The Chief's miraculous discovery and even performed several in-game sidequests related to them.
Hilariously Abusive Childhood: The Sangheli way of dealing with teenagers apparently involves sending them off to fight battles for the empire, figuring that a few near-death experiences will make them less uppity.
Heroes Prefer Swords: Invoked with the Arbiter, but also lampshaded and deconstructed by Miranda when she uses it to her advantage in her fight against him.
Hoist by His Own Petard: Garrus kills Dr. Saleon by locking him in a test chamber with one of the Flood infection forms he was experimenting on.
Hidden Depths: N'tho 'Sraom: Ascended Fanboy of the Master Chief, irreverant mid-battle singer, conspiracy theorist (of sorts)...and Warrior Poet (knowing human poetry—in N'tho's case, Shakespeare—is practically mandatory if you want to call yourself a Squidhead with a straight face). He's also written several thesis papers about alien cultures, and is able to hold a relatively sophisticated conversation about the sociological ramifications of the end of the Human-Covenant War, how it affected his species, and similar parallels in other races.
Hypocritical Humor: After The Chief is captured by Dr. Saleon, a turian guard falls for The Master Chief's "pretending to be passed out in jail" trick and gets close enough for him to drop the guy to the floor and snap his neck. The Chief then reads an email on the guad's omni-tool where he called a coworker a moron for wanting to try on the Spartan's armor.
Interestingly, also averted. He might not be too smart on the battlefield, but it's also clear that he's plenty smart in other ways. For example, he's working on an essay comparing asari writings to his own culture.
The Illuminati: Subverted. As per Halo canon, The Assembly helps guide humanity, but doesn't seek to rule them.
Chief is starting to show a very socially-aggressive side. His treatment of the Normandy crew is becoming increasingly cruel, even by his standards. See Kick the Dog entry below. He seems to be realizing this as of Chapter 32.
N'tho speculates one is afoot with the Chief at its center, pointing out rumors that the Chief is dating either Liara or Ashley, speculating that Kaidan may have a crush on him, and that even Tali might see something in him. The Chief and Kaidan insist otherwise.
Although Kaidan has admitted to "Admiring" the Chief from time to time, but says that it's purely from an artistic standpoint.
N'tho, as revealed in the same section, has read several articles on how quarian reproduction works...
Meaningful Name: "Ustrina" is the ancient Roman name for the site of a funeral pyre. An AI of the same name tries to kill The Chief's ground team by activating a Self Destruct Sequence on board the ship they're on. Before that, she helped Horridus program a nuclear bomb and several trap mechanisms to fool Cortana into getting The Chief's team killed. Furthermore, her avatar is wreathed in flames.
The Mole: Cortana winds up becoming one of these for the Assembly, much to her chagrin.
Mundane Utility: A Yanma'e (drone) is seen using her flight powers... to deliver pizza.
My Species Doth Protest Too Much: Chief meets an entire political movement of these, the "Slip to the Future" party. They're a salarian-founded group with many non-human members advocating lifting bans on Slipspace technology, which is a solely human invention.
For the Salarians, it's less of this, since their government voted against the Slipspace ban, but were outvoted by the Asari and Turians. Any Asari or Turian members are a straighter examples of this.
A lot of characters have similar thoughts about elevators throughout the entire series.
The Love Dodecahedron mentioned up above has Chief's possible romantic interests include Liara and Ashley as the prime contenders, with Tali as a possible one, and Kaidan as another possible LI. Liara and Ashley were the romantic interests for Male Shepard in the first Mass Effect game, Tali is one of the most popular choices for romancing in the second Mass Effect game, and Kaidan is a love interest for the third game.
The name of Spartan B-312 (Noble Six) is the same as the name for the default Female Shepard (Jane).
Spartan 051, Kurt, is described as having many of Male Shepard's characteristics, including the infamous trait of saying "I should go."
ODST Vanderloo suggests that Chief punch al-Jilani if she tries to interview him again, similar to how Shepard could in canon.
Never Found the Body: N'tho mentions the Sangheili insurrection against the Arbiter in Chapter 39, and how it ended with an orbital bombardment of Jul 'Mdama's last known location. 'Mdama was never found and presumed dead, but prolonged discussion about rumors of his survival all but hit you over the head with the probability that he will show up somewhere down the road.
Chief himself at the start of the story, on the basis that all thealiens he's encountered before then have been trying to shoot him. Ashley of course also has shades of this, but after a conversation with some of the other crew members seems to mediate her views a little bit.
Noble Bigot with a Badge: Master Chief also expresses discomfort at the idea of taking orders from aliens before and after becoming a Spectre.
No, Except Yes: At the beginning of Chapter 42, the author announces that the Chief will finally meet Shepard...sort of. It turns out he meant The Chief contacts an ODST Lieutenant named Mark Vanderloo, who's named after the Dutch underwear model on whom Male!Shepard's default appearance is based. He does allude to some of Shepard's more memetically famous attributes as well.
No Plans, No Prototype, No Backup: Captain Anderson mentions offhandedly that one of reasons no more Spartans have been made since the end of the Human-Covenant War was because all the data pertaining to their creation were destroyed with Castle Base during the events of Halo: First Strike.
Noodle Incident: The Arbiter's fight with Miranda in Chapter 33 is their third encounter during his hunt for Cerberus.
Kal'Reegar came back from his pilgrimage covered in blood, badly injured, with a suit that was ripped to shreds, and carrying a Gravity Hammer. When asked how he got said hammer, he simply responded "It wasn't easy."
Wrex got into some trouble on the planet Sanves once and had to biotically manipulate a corpse to get out of it.
When they argue about whether or not to reveal Cortana's continued existence to the crew in Chapter 26, the Chief loses his infamously laconic composure and tells Garrus that Cortana is all he has left. One of his lines even has an exclamation point!
Cortana pretends to be a VI when Garrus examines her storage chip on his Omni-tool. He eventually sees right through it, having seen enough documentaries on the Human-Covenant War to put two and two together.
She tries again at a later chapter on the whole team. Let's just say the bluff failed not even 5 minutes in; It is a VERY bad idea to do so in front of someone who's race's Hat is "AIs."
Obstructive Bureaucrat: While initially friendly towards the Master Chief due to his role in destroying the Covenant's hold over the Kig-Yar, Administrator Chok still blocks Chief's desire to head up to Peak 15 during the Noveria mission.
Offscreen Moment of Awesome: The Chief gets one in chapter 41. Just before the narrative cuts over to his crew, he's being tossed around like a ragdoll by a biotic Jiralhanae Chieftain (naturally). When his crew later reaches his location, they simply find him standing over the chieftain's corpse cleaning blood off his knife.
Oh, Crap: Dr. Saleon has frozen samples of The Flood in his lab on The Citadel.
Old Soldier: Averted with Master Chief, who is the same age as he was in Halo 3 despite chronologically being 172 years old. Played straight with The Arbiter.
Miranda also seems to have this mentality, believing that it's okay to perform unethical experiments on people if they're violent criminals that no one will miss.
Percussive Maintenance: Inverted. Wrex smashes one of the nuke's hard points just in time to stop the detonation. He then refers to this trope as "Krogan Engineering."
Pet the Dog: Once he has some time to think about it and cool down, Chief starts making up for all his Kick the Dog moments, starting with giving Tali information on Slipspace technology for her pilgrimage.
In true Mass Effect fashion, these hats come off quite often, and with the Covenant races to boot. Most prominent is N'tho, a Sangheili Spec Ops warrior who acts unusually informal and Crazy Awesome compared to the Elites we've seen in Halo canon. Likewise, while the few other hats have come off prominently, Kig-Yar, the Goddamned Bats of the Halo franchise, have settled into more benign mercantile professions...such as lawyers.
When Chief first gets to the Presidium, he notices a Drone/Bugger/Yanme'e flying through the air... delivering pizza with an advertisement for her workplace draped over her.
When Ashley calls Wrex out for not identifying the Rachnai on Noveria, saying that the Krogan were the ones to wipe them out, Wrex turns it back on her by saying that while, yes, they did, it was two thousand years ago, and Krogan written records aren't all that impressive to begin with, so he had no idea what they looked like other than "Bugs," helpfully inverting a few of the Warrior Race tropes.
Master Chief: The Forerunners are not gods. They did not ascend to a higher plane of existence. They were wiped out by the Flood. They didn't want you worshiping them or the broken toys they left lying around, and they sure as hell didn't think your species was somehow unique from the others. You know how the Forerunners really saw your species? You know what they really saw when they looked at you split-jaws a hundred thousand years ago? They didn't see the beginnings of a noble race of warriors. They saw a race of savages who were still trying to get the hang of making fire, and didn't stand a chance against the Flood. They didn't ennoble you with some kind of divine destiny. They took pity on you. Now, we're on a high-profile mission to track down a rogue Spectre and bring him to justice, which means we don't have time to entertain an ancient squidhead fairy tale. Are we clear on that?
Retcon: There was a period of time when the author couldn't decide how to mingle the two timelines together. At first, the Halo verse was bumped up a few centuries, with the story taking place in ME time. Then the story was in 2683, for no reason. Then bumped to earlier, with the author justifying it by pointing out how the technology present in Halo would be more along the 2100's. Then finally, it seemed to settle on 2683, because it would be impossible to colonize 800 planets in 70 years, and instead moved the Mass Effect universe up 500 years.
Rule of Cool: Vanguard Hunters. Justified because it's a giant alien monster the size of a truck that decides that something over there really needs to die, and then BAM, he's slamming into that something at unbelievable velocity. It's a terrifying combination.
Sabotage To Discredit: Chok and his mercenaries did this to the Turian slipspace ship to render slipspace technology illegal in Citadel Space, primarily for financial reasons. Specifically, if Slipspace Tech was banned in Council Space, then Noveria, which sets itself up as a world where Council Laws don't exist and all varieties of scientific research are welcome, then the only place that further Slipspace research could take place was on Noveria, lining his pockets.
Screw the Rules, I Make Them!: A general ability of Spectres except with the Council, Chief uses the privilege to leave a star system earlier than ONI wanted him to.
Meta example. The Jackal's beaks are this to the author, and according to him prompted him to refuse to recognize anything from Halo 4 (except the Prometheans) in his story.
It's not clear how serious he was with that statement, as weapons and vehicles (as well as characters) have had references made to them or actually appeared, including the Mantis mecha, the SAW (Squad Assault Weapon), and a Rail Gun.
Shaggy Dog Story: Possibly. The Arbiter spends Chapter 33 hunting Cerberus on Omega and although he fails to download intel from any of their computers, Miranda hands him a datapad (supposedly) containing information on The Reapers, Saren and the Geth. He immediately destroys it without even reading it, presuming to to be booby-trapped or at least bugged. Correctly, as Miranda casually reveals in the next chapter.
Shoot the Medic First: Chief's team is forced to destroy a drone that kept restoring the shields of a juggernaut before they can kill the large Geth.
The next chapter has Cortana alter her appearance so anyone else who sees her won't think she's the Cortana. Among other changes, her avatar color is now pink. When a dumbstruck Chief points this out, Cortana replies that she thought it was "lightish red."
During a firefight on Feros, Wrex shouts "Get over here!" when using a Biotic Pull on an enemy.
During the battle against the Thresher Maw, N'Tho yells a line "From Hells Heart I stab at thee, bitch!" This could either be a reference to Star Trek II or to Moby-Dick, which the line is originally from.
In chapter 25, when Garrus accidentally calls Ashley fat, he imitates Freeza unknowingly.
Garrus: Oh look. That creeper died. And several more live ones are over there. Could we go deal with that? We'll continue this conversation never.
Chapter 36 has Tali visit a nightclub... which is a massive shout-out to the "Seige of Madrigal" Easter Egg from "Halo: Reach," including dancing unggoy and a jirlhanae DJ.
Chapter 37 is a massive shout-out to the Halo multiplayer community, and more importantly, to Rooster Teeth. Geoff and Jack are the commentators, and the "Achievement Hunter Rodeo Clowns," segment is another large shout-out to Rooster Teeth's infamous Lets Plays of Minecraft. It even includes the trophy for that game as one of the objectives (known in this story as "Pillar of Vitality," because "there are kids in the audience." (The real name for it is "The Tower of Pimps."))
Chapter 38 has an ONI operative, "Brigadier Lethbridge-Stewart," clearly based on the character from Doctor Who.
Chok likes to channel Andrew Ryan a lot, particularly when he gets arrested.
Chok: A MAN CHOOSES!!! A MACHINE OBEYS!!!
Space Jews: In addition to the Volus, any Kig-Yar who haven't gotten jobs in the military or piracy fall under this trope, having become shrewd businessmen and lawyers in the last century. Some Unggoy are said to fall under this trope as well, but the majority can be considered Space Mexicans, as they are a source of cheap labor.
In chapter 10, the Chief comes across Garrus fiddling with the Mako. When pressed, Garrus said he thought the Mako's suspension was off and needed adjustment...another word for calibration.
According to The Guardian, The Forerunners classified the Turians as "Species Delta-702" and the Krogans as "Species Delta-1404," implying that Krogans are basically twice the creature a Turian is.
Summon Bigger Fish: Of the "instantly backfires" variety. In chapter 28, a group of mercs release a Flood Tank Form from containment to have it deal with Chief and company. Liara tosses it across the room, to have it deal with the mercs.
Tali decides to drive with the Chief, thinking he can't be as bad as N'tho. It doesn't work.
See the "Drives Like Crazy," entry for more details.
N'tho invokes this on Noveria by thinking that the team won't encounter any monsters, twisted experiments or anything like that. Made even worse when he adds "probably" after that list.
Terms of Endangerment: Of a sort. It's worth noting that, thus far, Saren is the only character in the fanfic to consistently refer to the Master Chief as simply "John." Partially because Saren refuses to give a heroic honorific like "Master Chief" to a Human, partially because Saren knows that it gets underthe Chief's skin.
Then Let Me Be Evil: The attitude that Ustrina has in regards to the Council's distrust of AIs. Chapter 41's codex entry also implies that other AIs in the Terminus carry this attitude as well.
Time Bomb: Chief's team is almost killed by a nuke on a timer.
Title Drop: Twice so far. First when The Chief visits a memorial to his fellow Spartans and realizes he's the last one. A second one comes when Sha'ira advises him to open up more to his crew, telling him that by doing so (read: acting like a proper Western RPG protagonist) he will "no longer feel like the Last Spartan."
Token Evil Teammate: Invoked by Miranda when speaking to Kai Leng, asking him if all of the ODS Ts were as bad as him or if he was just an exception
Averted unlike the Halo series. Since Master Chief is filling in for CommanderShepard, he's spoken more in his first two chapters than he has in the Halo Trilogy. Played for Laughs as he still uses short, blunt sentences where Shepard used charismatic lines, and complains silently about how sore and raspy his throat is becoming.
Althought technically this was subverted in the series itself- Chief actually did speak in the series... it's just that he didn't do it all that often, and was usually in short, to-the-point sentences.
Warrior Poet: We already know Ashley's one, but both she and Master Chief are surprised when N'tho shows off his knowledge of Tennyson and Shakespeare. He reveals that it's practically a requirement for the Squidhead subculture.
Well-Intentioned Extremist: The Assembly has shades of this, preferring to set off the incident that banned AIs rather than risk a major war with the Citadel Races against the Systems Alliance.
Wham Episode: Chapter 18. Chief has been kidnapped on what he now learns are orders of Saren. The Arbiter is launching a rescue mission with Garrus. Cortana is missing. And to top it all off, Saleon is working on the Flood.
Miranda mocks the Arbiter of this when they fight in chapter 33, how despite him having guns he still relies on his sword. Averted the very next instant, as the Arbiter then opens fire on her with said guns, forcing her to take cover.
He then reveals that he was deliberately not using it until she suggested it or pulled out her own gun, as that wouldn't be honorable. It's at this point that Miranda plays this trope straight and pulls out her own gun.
The Human/Former Covenant Alliance defeated the Turians at Shanxi and eventually joined The Citadel as in one half of the source material, but were eventually forced to reduce the size of their fleets and give up Artificial Intelligence and Slipspace technology in the process, as their new peers thought them too dangerous.
In practice however, they're still fighting "the peace." They're exponentially more aggressive in their efforts to become a Council race in TLS, with the stated goal of re-introducing AI and Slipspace once they gain the Council seat(which coincidentally would permit them to triple their fleet size.).
It's also noted that human colonies outside of Citadel Space do use AI's and slipspace drives, because they are not ruled over by the Citadel Council.
Although no one says it to the Chief himself, Harkin and Saren (understandably) don't think John is the real McCoy, and is just an unusually tall soldier they put in similar armor as a publicity stunt.
Ethan Jeong is unimpressed when the Chief states he swore an oath to protect Earth and its colonies, and unlike the above two examples, openly calls the Chief a phony. The Chief's response puts him in his place though.
Alien Arts Are Appreciated: Not so much art as a whole culture, but a Mormon Church features at least one Sangheili and one Elcor in its congregation.
Always Someone Better: Lieutenant Nolan is a bit put out when The Master Chief effortlessly breaks his previously unbeaten record on the firing range, and loses sleep trying to reclaim it.
Ascended Extra: The Marines that thawed out the Chief in Chapter Two of the original fic? We get to see what they did before and after too.
Odd Name Out: Kyle Nolan and Corporal Timothy Michaels (the latter of whom was the only Marine named in the original fanfic) are the only (purely) anglophone names among a Badass Crew with names like Tu'uta Tangilanu, Julianne Engelbrektsson and Asha Beckett.
P.O.V. Sequel: Chapters 3-6 are actually the second and third chapters of The Last Spartan from the point of view of the Marines who personally thawed out The Master Chief.
Reporting Names: During the First Contact War, Turians were initially dubbed "Raptors" though a few other Marines came up with names of their own, such as "boneheads" due to their skull-like faces. The former name has since become a Fantastic Slur.
Shrouded in Myth: One of the soldiers recounts their grandfather believing til the day he died that Spartans were actually robots.
War Fic: The first two chapters feature Kyle's first hours on Shanxi during the attempt to reclaim it.