Initially discussed and averted; Matt clarifies to Zheng that X-Com wants to kill the aliens only because those aliens attacked them first, and not because of their being aliens.
Supporting this viewpoint, in Supplemental Files 6, Bradford officially drafts and releases new operating procedures to account for the definite possibility of more Equestrians arriving, giving grounds for a non-hostile contact.
Then double subverted when several Strike leaders cheerfully express xenophobia in chapter 29 and drag Matt and Lana into the crossfire for their "exposure".
Lieutenant Kato, Strike Seven: "I sure as hell know that I’m not risking my neck or Strike Seven so some furry freak can live here like we’re a hotel. We’re here to— —kill every last one of these aliens.”
Comes up again in chapter 34 when a senior interceptor pilot can't believe Vahlen wants to save Twilight despite all that the latter's done for them.
Actor Allusion: The fic gives the first-nameless support staff first names. David Bradford is played by David Hoffman. Moira Vahlen is played by Moira Quirk. And Charles Shen is played by...um, François Chau.
For one, more than a single squad is deployed on most operations, the Gangplank operation seeing 6 Skyrangers full of soldiers seeing action, and the Skyrangers also provide covering fire for the attackers.
The mundane activities of the base personnel and research also get more focus, as it was largely just reading research reports in the actual game.
Operation Gangplank in the game ended with destroying power conduits on the surface of the alien battleship. Here, the troops must actually penetrate the ship and secure both the bridge and the engine room before it can be controlled.
Alien Arts Are Appreciated: Food from Equestria is apparently super-delicious to humans, which makes Pinkie Pie's desserts very appreciated amongst the Stardust team in chapter 20. This isn't just a case of Pinkie Pie being a Supreme Chef, either; in an early chapter, Lana finds a piece of fruit transmuted into an Equestrian apple to be extremely tasty. Reviewers have commented this could just be because Army food tends to be bland as a rule of thumb, so anything tastes better after living on it.
The three Alicorn Princesses are believed to be immortal tyrants — especially Cadance, who is believed to use her love-related powers to Mind Rape the populace into compliance.
As of Supplemental Files 6, though, Dr. Mills is of the official opinion that Celestia, at the least, is quite restrained in the usage of her powers, so she isn't quite as much a source of fear as they had figured.
In chapter 22, the base psychiatrist suggests to Twilight that Discord may be so crazy due to the deleterious psychological effects of spending a thousand years as a conscious mind trapped insidean inanimate stone body. Twilight herself considers the idea with some unease before taking the stance she still can't forgive Discord for what he did to her and her friends, even if he has been driven insane.
Always Someone Better: The sleeker look of EXALT's laser weapons? Not just cosmetic. The weapons are smaller and lighter than XCOM's, even if the batteries have lower absolute capacity. After examining some captured ones in chapter 32, Shen takes it as a personal challenge.
Anti-Villain: Dr. Moira Vahlen. While she comes off, even In-Universe, as a Jerk AssMad Scientist, she does have valid concerns. Twilight Sparkle has so much telekinetic power she's like a walking A-bomb that can detonate multiple times, she can teleport practically anywhere at will, turn invisible and inaudible, perform spells that compel individuals to violently attempt to gain possession of a target she designates, and she seems to just keep coming up with new powers. A hostile Twilight Sparkle would be a nightmare to face. As proven in chapter 33.
Anyone Can Die: As is usual in X-COM, being a named character does not protect you from horrible death. Lana (she got better), Dryzimski in chapter 30, Kim and Joel in chapter 33.
Ascended Extra: For a very short time, Matt and Lana were literally nothing more than nameless, faceless soldiers. Matt was the random guy who captured Twilight, while Lana was joking around shortly before Shen met Twilight. They soon became the main points of contact between Twilight and XCOM.
Averted by Dr. Mills, who notes that his initial gut reaction is to dismiss such a story, but then reminds himself he's talking to a purple unicorn on the topic of magic, and so she might just be telling the truth.
In chapter 26 Dr. Shen notes that the engineering staff who had seen so much previously thought impossible reached the breaking point when invisibility devices were broached.
Badass Adorable: Twilight Sparkle — cute enough that even a hardened female X-Com soldier starts squeeing like a little girl over getting to be a contact with her, and with enough telekinetic power to not only smear a Chryssalid with a thought, but to blast apart the containment unit that X-Com performs its "interrogations" in. Keep in mind, this same unit in-game holds everything from the Ethereals to Muton Berserkers.
Chapter 33 puts the emphasis on the badass part, when Twilight pretty much singlehandedly annihilates the enemy invasion. This includes shrugging off direct-hit plasma blasts from alien spaceships.
Badass Normal: Pretty much every recruit in X-Com, in theory. Robert Sachs, a new recruit from the Australian Tactical Assault Group introduced in chapter 24, is a stunning example. He got recruited for killing a Chryssalid. With a knife.
Empowered Badass Normal: Chapter 28 reveals that this is going to become endemic amongst X-Com, due to Twilight's presence; because she's been "loosening up" the native Field, it's becoming increasingly easy for humans to access it. Meaning more mages/psykers are "awaking" due to that ease — and as they "massage" the Field in turn, it will become even easier, meaning even more people will gain the abilities. Lana, Matt and Bradford are all confirmed as having "awakened" so far.
In chapter 14, a captured Thin Man just flips the fuck out when it sees Twilight, starts making death threats and beats itself to death trying to get out and presumably at her.
In chapter 20, another soldier makes a poor choice of insult to an already-steamed Lana, and Lana makes him pay for it.
In chapter 32 we learn Vahlen really hates traitors to humanity.
Beyond the Impossible: In her trans-dimensional letter to Twilight, Pinkie Pie manages to include enough pastries for every researcher in the Stardust project while managing not to squish them in the rolled up paper. Even after reviewing security footage, everyone is stumped how it happened.
Big Brother Instinct: Shining Armor makes a point of questioning Matt about how close he is to Twilight.
In chapter 33 the Overseer Ethereal was about to capture Twilight when someone killed it. In chapter 34 it turns out to be Zhang using his LANC.
In chapter 34 Luna and some guards were about to attack Matt and co. before Discord saved the latter by greatly shortening the countdown on their teleport back to Earth.
Blazing Inferno Hellfire Sauce: Pinkie Pie's special hotsauce, which is the immediately assumed ingredient in the cupcake she gives Spike in chapter 18, though he thinks she may have added some crushed "inferno rubies" as well. How hot is it? Spike, who swims in molten lava and actually thinks the "baked bads" that leave Pinkie sick in bed are yummy, finds it too spicy to handle.
In chapter 10, which is the first look back at Equestria after Twilight is vanished, it's revealed that Discord has not done anything (even moving) since sending Twilight to Earth, even calmly allowing Luna and Celestia to erect what should be a prison around him. Why? Because he's waiting for Twilight Sparkle to to fulfill her end of the bargain.
In chapter 22, Discord is horrified at the idea of bartering for or stealing souls from other people, because "The soul of a living creature is the purest spark of creativity and change in the universe. It is change, it is hope, it is the drive that every little living thing needs to motivate themselves to get up in the morning and take on the world, or at least their horrible commute and coworkers." Despite this, as fans of the canon are well aware, he sees no problem with doling out Mind RapeFor the Lulz. In the same chapter, he also restores Lana to life because he wants her to keep being Twilight's friend.
Continues in chapter 31, where Discord chides and scolds Celestia to her face, for much the same reasons as in chapter 22, then turns around and terrifies the hell out of a changeling acting as a conduit for Chrysalis for celebrating his "weakening" of the ponies.
In chapter 34 he helps the Strike team sent to Equestria to return Twilight escape, which confuses at least one Council member who was led to believe by Discord's previous actions that he would have actively hindered Twilight's return.
Break the Cutie: Twilight's gotten a continuous chain of these in the early chapters, starting with witnessing a Chryssalid slaughter some civilians, then having to kill it in self-defence, and going on from there. It happens again in chapter 33 when she recalls Lana and Matt fighting the EXALT infiltrator and starts wondering if Shining Armor also has a killer within.
Twilight seems on the way to becoming this; she's had several really bad nightmares about the events of the first few chapters, and in chapter 14, she has a PTSD-style flashback to the Chryssalid attack upon being confronted with a spider.
Confirmed for Vahlen in chapter 17; her family were killed by a Chryssalid in a Terror Attack while she was listening over the phone.
Brought Down to Badass: In chapter 31, Celestia asks why Discord doesn't "release her" so she can protect Equestria from the incoming alien invasion, implying that he did this to her. Discord refuses by declaring she'd become just as great a threat to Equestria if he did. Fortitude Amicitia gives a strong hint as to why he sealed off some of her powers in the first place.
Vahlen's cold, provocative attitude is really not the smartest one to take when she herself notes that X-Com couldn't hope to build anything that would stand up to Twilight's telekinetic blasts. Fortunately, she eventually grows out of it.
Made even worse by the fact Twilight has, and has explained to X-Com that she has, very close social bonds to Princesses Celestia and Luna, either of whom is powerful enough to make Twilight look like a stage magician... and Twilight is pretty damn scary compared to humans as it is. If they come to Earth looking for Twilight, and find she's been Mind Raped and dissected, it would not be good for X-Com.
Lampshaded when the two volunteers agree that they thought a scientist like Vahlen would be "smart enough not to try and brow beat a test subject that could reduce her to a red stain and an unpleasant memory with a thought".
Played for laughs in chapter 14; Lana thinks it's a good idea to tease Twilight about her crush on Matt. The unicorn is not amused and promptly zaps Lana with a minor hex that temporarily obliterates all noise that Lana makes, effectively putting her on "mute".
Then the same thing happens again in the very next chapter. Twilight muting Lana might be on its way to becoming a Running Gag.
Invoked in chapter 17, when Vahlen points out Twilight's connections to her homeworld's royalty, and the potential power level thereof, when she revises her recommendation from cancelling Project: Stardust to keeping it running.
Burning with Anger: According to chapter 10, Celestia nearly vaporised her throne room when she got Spike's message that Discord had just vanished Twilight to parts unknown. She's still blazing hot enough to crack marble and disintegrate carpeting when she teleports back after confirming this.
Twilight in chapter 33 leaves behind hoofprints melted into the floor of the X-Com facility when she goes berserk.
The Butcher: Episode 24 reveals that Matt has this nickname in the media, from the incident where he had to shoot an insurgent Child Soldier that he brings up in chapter 14.
Logical Weakness: Because it's not true invisibility, instead a sort of hypnosis, it doesn't work on machines. Like, say, Cyberdiscs...
Canon Welding: The fic was well underway before Enemy Within for XCOM was even rumored. Now that the expansion is released (much to the author's enjoyment), new developments such as Meld and EXALT are being introduced into the story.
Car Fu: In chapter 33 a SHIV rams a Mechtoid to bring it down.
Cardboard Prison: Discord is still capable of wielding large amounts of power in spite of Celestia's custom-built prison. The main reason why he doesn't just escape is due to keeping his end of the deal with Twilight.
Chekhov's Gun: An early comment by Twilight is that the native "Field" is stiff and musty from disuse, but it'll loosen up as she uses it more. Come chapter 28, and The Reveal that a side-effect of a "loosened" Field is that it becomes increasingly easy to touch, meaning X-Com members are starting to spontaneously develop powers of their own as they can begin to access it.
The Chessmaster: Discord. He was aware of the alien threat from the very beginning, and all of his actions had been geared toward securing the humans' help for when the invasion of Equestria happened.
Combat Clairvoyance: Bradford has this ability. He's quite disturbed by it, partly due to the strain it causes.
Composite Character: Bradford here is a composite of the original and the player-controlled Commander.
Crapsack World: From what the newbies said in chapter 24, the world outside XCOM looks pretty bad.
Twilight vs. Chryssalid; Twilight squishes the specimen of the In-UniverseDemonic Spiders with literally nothing more than a thought.
Twilight vs. an army of aliens and EXALTs; Twilight destroys every synthetic and petrifies every living opponent she faces, until she encountered the Ethereal Overseer.
Cyborg: Twilight designs cyber-prosthetics for maimed soldiers after Lana gets her arm cut off. It's implied she's used certain "spell-circuits" related to golem construction to get around some of the logistical problems invoked by this trope.
Cynicism Catalyst: In chapter 15 it's strongly implied that something bad, probably alien-caused, happened to Vahlen's family to make her the cold, paranoid jerkass she currently is. Confirmed in chapter 17; Vahlen's family were killed by Chryssalids in a Terror Attack, and she was on the phone listening as they were slaughtered.
Dark and Troubled Past: Everyone at X-COM. Twilight might also qualify, though it's not exactly in the past yet.
Death Dealer: Inadvertently happens in chapter 29 when Lana's testing of Matt's telekinesis with playing cards goes awry.
Dirty Business: After some squad leaders protest about the limited distribution of Wallflower "equipment" in chapter 22 costing them the lives of many men, Bradford lies about its true origin in order to protect Twilight, feeling distasteful about it all the while.
The first Ethereal, also in chapter 33, psionically overpowers Twilight with two words.
The Evils of Free Will: In chapter 31 Discord claims that the Elements of Harmony would fail against the Ethereal invasion because the Ethereals and their slave races adhere to their own twisted sense of Order.
In the same chapter, he makes it clear that he believes that Celestia herself would fall into this if he "released her". Fortitude Amicitia, revealing as it does the existence of a "Queen Solaria" who engaged in rampant petrification of ponies for the most petty reasons, implies that he believes this because she already went this route before.
Twilight wasn't being facetious when she said about the spell she cast on Matt and Lana: "“If it works out right, nopony will notice anything”. The spell is basically an invisibility spell that works by causing others to not notice anything the target does.
Luna told Discord to leave 'this place' and never return, but failed to mention actually leaving Earth.
Face Palm: Matt frequently does/feels the urge to do so in response to the the antics of those around, especially Lana.
False Flag Operation: EXALT is in the preparation for these in an attempt to discredit XCOM, confirmed by Word of God. They've managed to acquire a Skyranger and first-generation XCOM combat uniforms, intending to run equivalent Terror! missions against cities to incite panic.
Foreshadowing: Early on, Shen tells Twilight that "When we are afraid, we lash out at the cause." In chapter 33 a scared soldier mistakes her for a hostile and shoots her.
Freudian Excuse: Lana has one for her fixation on the importance of hope — hope was all that helped her get through her life when her coming out as a lesbian caused her father to explode in a fit of violence, resulting in him then turning on her mother and Lana having to shoot him to prevent him from killing either of them, and the resultant consequences of that shooting.
Joel wonders in chapter 23 if the spell Shining Armor and Cadance used to drive the Changelings out of Canterlot crushed any then-indoors Changelings between the spells and the walls.
Dr. Ngo wonders just what kind of hellish experience Twilight's childhood must have been if she was first taught by royalty AND babysat by royalty, only to then be brought into the royalty by marriage.
Bradford's mind evidently goes somewhere horrible when Twilight explains that people developing magical/psionic powers is going to become a chain reaction; he immediately orders her to design and build blockers to prevent such awakenings.
Gas Leak Coverup: Widely used by the Council to explain away alien attacks in the early months of the invasion, and even used by XCOM to recruit soldiers/pilots from the regular military. Vic Spiegel is a specific example.
Grenade Hot Potato: Matt does this in episode 9 with an alien grenade, ensuring no casualties, but getting himself seriously wounded; he's lucky not to have wound up paralysed or dead. Justified in chapter 28; his exposure to Twilight's magic is starting to awaken telekinetic abilities of his own.
Golem: Equestria apparently used to have them, as Twilight immediately starts recalling the stories of them after being given information about the Cyberdisk. They've been illegal for a long time, though.
Gone Horribly Right: When parallels between a material from Equestria's past and Elerium were pointed out in a letter from Pinkie Pie, they try to test an Elerium sample for magic reactivity with a levitation spell. The sample punches through the ceiling, through the mess hall (almost killing Joel), through the rest of the base, the ground above them, and eventually hitting a reconnaissance satellite. Turns out "Arcanite" fundamentally enhances any spell cast on them, so using telekinesis means a super-kinetic surge; they were expecting it to glow because that was the first documented spell cast on Arcanite.
Gory Discretion Shot: The end of chapter 31, where Discord goes full Lovecraftian on a changeling acting as a conduit for Chrysalis.
Had To Be Sharp: In chapter 31 Discord claims this of mankind, pointing out how they had to struggle on their own against their uncaring universe without magic or a benevolent deitylike being actively guiding them.
Heroic BSOD: Twilight undergoes one that last for about a week after Vahlen tries to force her to display her telekinetic offensive abilities.
Heroic RROD: Twilight pushes herself to extreme measures to obliterate as many Ethereal forces as possible. Her medical reports suggest that the strain from such a feat means she possibly can't do anything similar in the future.
Hope Spot: Discussed in chapter 20: Shen reprimands Lana for making Twilight think that Matt's romantically interested in her, saying that this kind of false hope will only make things worse once the truth comes out. Lana insists in retort that false hope is better than no hope.
Humans Are Special: Discord believes this to be the case due to their inventiveness and stubborn will to do seemingly impossible tasks.
I Need a Freaking Drink: In chapter 27 Frank takes a swig of liquor straight from the bottle after the Ea reactor nearly goes critical.
If I Wanted You Dead...: In chapter 30 Discord claims that he wouldn't have done this roundabout sending Twilight to Earth thing if he really wanted her dead.
Implacable Man: The first appearance of a Mechtoid in chapter 33 has it as this, tanking fire that at least two Mutons and six Chryssalids are shredded by thanks to its Deflector Shields.
In chapter 33, when a Mechtoid isn't affected by Twilight's petrification spell, she telekinetically throws a vault door at it. Both it and the door go through four walls before finally being stopped by bedrock.
In chapter 34, we see in flashback that Twilight managed to petrify another Mechtoid and use it to batter down the shields of a third.
Interspecies Romance: Apparently, it's fairly common in Equestria, in part because there are an average of 3 stallions to every 7 mares. Upon hearing this, Lana immediately figures the best way to give Twilight a better problem to occupy her mind with is to tell her that Matt thinks she's cute. Fortunately for her, Twilight is both a naive virgin and unaware that Matt was the soldier who captured her for X-Com, so given the context in which Lana mentions it, it's not that surprising Twilight starts thinking she may have a human would-be suitor. Twilight turns Matt down on the grounds that she's not ready in chapter 24, with Matt being relieved, as he was trying to find a way to let her down first.
Irony: The very soldier who catches Twilight for X-Com ends up being assigned to her as a "friend", and she firmly trusts him, to the point that she eventually starts believing he has a crush on her... and seems to be reciprocating.
Ironic Echo: Vide wrote "We will be watching" on the wall of his cell, a phrase commonly said by the Council after their briefings.
Vahlen and, as we learn in chapter 15, the Council, though chapter 16 shows the latter are far from unanimous comes off as unnecessarily nasty to those of us with outside knowledge, but she does have a point; Twilight is basically an Eldritch Abomination, no matter how cutesy-adorable she is, and she could pose a serious threat to the survival of the human race if she starts using her powers against them. A bit of paranoid suspicion is quite justifiable.
Invoked/lampshaded by Commander Bradford, though even he thinks Vahlen is letting her paranoia run away with her common sense, and gives her some pointed advice on the subject in chapter 11.
Knight of Cerebus: In-Universe, Vahlen deliberately tries to use Zhang to shake Twilight out of her cosy world-view in hopes that this will make Twilight more "productive" in terms of providing useful information, etc, against the invaders.
Spike's "messenger fire" explicitly uses a different form of magic to that used by the ponies, according to chapter 18. In fact, Spike's fire messages are technically a form of Sympathetic Magic, relying on Spike's familiarity with the targeted individual and/or destination. This is how they were able to send the messages in chapter 17; Luna helped guide Spike, the Mane 5, Cadance, Shining Armor, Princess Celestia and herself in using The Power of Friendship to boost Spike's messenger fire and let him send the messages to Twilight, despite not knowing where she is.
Averted with Equestrian magic and X-Com psionics, however; all evidence so far is that "psionics" is just a particular branch of magic, and Twilight can easily recognize alien "spell-circuits" due to their resembling runes and the like from Equestria.
Major Injury Underreaction: In chapter 21, Lana takes losing her left arm surprisingly well. The fact she's bleeding out, in physical shock and dies moments later probably helps her keep her cool.
Mama Bear: The Princess's response when XCOM sends a team to return Twilight to her home world is... excessive, but there can be no doubt that it was out of concern for her safety.
Metaphorically True: Lana and Matt use this trope to describe the "specialist" that will help train XCOM's latent magic users. They say that "she's a little girl that comes up to your waist," "she's extremely sensitive," and "despite her outward appearance, she's just like us on the inside." Extremely truthful, but the trainees don't find out that Twilight is an alien girl until they actually see her.
The Mole: It's strongly suggested that EXALT has at least one within the Council.
Happens a lot, given this is a serial mixing an animated series about cute talking ponies with a game about violent, paranoia-inducing alien/human warfare.
In Chapter 32, Twilight is watching a Harry Potter and the Philosopher's Stone movie with her friends moments before Vide barges in and tries to kill them.
Bradford and Princess Luna's solemn meeting takes a turn for the comedic when Discord interrupts by noisily drinking a soda.
Moral Guardians: Invoked in that when Twilight is given internet access in chapter 15, everyone thinks it's a good idea to restrict her access to certain topics that could lead to unpleasant questions or reactions, like religion, warfare, sex and geography.
Psychiatrist Dr. Frank McKendrick warns in his report in Supplemental Files 6 that X-Com should take every precaution not to discuss outright offensive applications of Twilight's powers/knowledge where she can hear, as she is likely to react very badly to the thought of being used for things that are not defensive or utilitarian in purpose.
Mundane Utility: A lot of Twilight's powers, to the bemusement of X-Com. Telekinesis that can crush a Chryssalid to a smear in one shot or drive solid steel two inches into solid rock? She uses it for tidying up after herself. A spell that renders the target completely silent, so even their actions make no noise? Perfect for silencing an annoying woman teasing you. Inverted in that X-Com is at least considering trying to weaponise any spell that seems it might be useful.
Happens again in chapter 20, she is quick to caution Vahlen and the others not to try and figure out how Pinkie does the things she does, citing her own disastrous attempt at doing so.
In chapter 11, Twilight confirms that her "Wallflower" spell she used to protect Matt and Lana is basically an inversion of the "Want-It, Need-It" spell.
In the bonus "What If?" chapter, after Fluttershy forces XCOM and the Aliens to stop fighting, the Council Leader's dialogue when shutting XCOM down is identical to the Non-Standard Game Over in Enemy Unknown, complete with the odd phrasing indicating mind control.
The pin-up photos of Twilight Sparkle are noted to have her making "bedroom eyes," which Matt surmises were simply lucky frames from a high-speed video camera while Twilight was mid-blink. This references the MLP fan trend where episodes are paused for the◊ same◊ effect◊.
In chapter 15 the Council considers having Twilight sent to the Argentina base for further interrogation, a reference to the bonus for locating your base in or having full satellite coverage over South America being instant completion of interrogations.
In chapter 18, Spike gets a super-spicy cupcake from Pinkie Pie and thinks she's used her "special sauce", clearly referring to the hotsauce cupcake that Pinkie ate in the first episode.
Neck Snap: Vide kills several X-Com operatives in this manner.
Non-Lethal Warfare: Deliberately invoked by Matt's team to avoid an interplanetary incident on their mission to Equestria, nearly subverted when they came under attack but played straight when Discord intervened.
Noodle Incident: The only thing known about the SHIV's encounter with Pinkie Pie is that it came back to Earth covered in various party supplies.
Not so Above It All: In chapter 15, Dr. Vahlen finds herself twice reprimanding herself and having to rework her latest reports to dehumanise Twilight after absent-mindedly using her name and feminine pronouns throughout the reports.
Not What It Looks Like: Chapter 14, Lana walks in on Matt cuddling Twilight (he's comforting her over her Chryssalid-related issues — somewhat involuntarily; she hugged him first and he's under orders not to touch her without her permission). Naturally, she can't resist teasing him about it.
The X-Com scientists, Vahlen, Mills and Ngo, all get one when Twilight freaks out at the approaching interrogation machines and teleports out of the containment cell.
Twilight gets one when she not only realizes that further tests will have to be with the cold, scary Vahlen instead of the friendly humans who have been interacting with her thus far, but remembers that two of her "new friends", Mills and Ngo, were standing right alongside her when she was about to painfully interrogate her.
Mills gets one in literary form when he realizes that Twilight has remembered what he and Ngo were party to and she no longer trusts them.
Luna (and everypony present, if we're honest) gets one when they see Princess Celestia is seriously ticked off by what Discord has done.
Matt gets one in chapter 30 when the Sectoid Commander pulls the knowledge of Twilight's existence from his mind and presumably sends it on.
The first experiment with Elerium and magic was this. They wound up punching a hole through the entire base, and took out a satellite.
Matt and his team get this reaction when they see how angry Celestia is over Twilight's injuries.
In-Universe, chapter 8 has Matt and Lana note how earth-shatteringly strange it was to see Chief Engineer Shen not merely angry, but livid, when he is normally the affable, easy-tempered member of X-Com's hierarchy, to the point he's considered the base's resident Santa Claus.
In chapter 30, Matt is worried when Fujikawa breaks radio silence sounding scared.
In chapter 33, Twilight recalls Lana's face having "an emotion Twilight could not comprehend or describe" when the latter was about to beat the shit out of the EXALT infiltrator. It only grows more pronounced when Matt and Vahlen start "acting up".
Twilight Sparkle is this, In-Universe, to Dr. Vahlen. She's cute, adorable and harmless looking to the point even other X-Com members want to trust and comfort her... while, at the same time, being incredibly powerful, with "Psychic Powers" that include possible Mind Control, teleportation, and sufficient Mind over Matter that she can tear through the thickest defenses X-Com can build. The best calculations that X-Com has suggests she could probably destroy headquarters singlehandedly, and nobody else seems to think she's a threat. The Reveal that she can alter perceptions doesn't help. After chapter 17, though, this seems to be dwindling.
Chapter 28 gives some to Commander Bradford, apparently: he immediately orders that Twilight start making "awakening blocking" devices upon finding out that more and more people are going to keep developing powers.
In chapter 34 a Council member wonders how long Discord may have been interfering with Earth.
Lana is well known for these. During her conversation with Matt in chapter 24, she drops some real groaners of hand and arm-related puns. Crosses over with Black Comedy because she's making those puns because of her own severed arm.
In chapter 24, Twilight also makes a bad joke about the research team losing the prototype artificial Wallflower module (as in, the device intended to make itself and whoever it's applied to invisible).
Private Military Contractors: Mentioned but Averted. News reports mention how analysts expected the industry to be booming due to the wealthy wanting protection from alien attacks, but the major contractors claim there's "a shortage of experienced operatives." Likely due to being recruited to XCOM, see the entry for Fridge Brilliance.
Pyrrhic Victory: Matt considers the raid on the alien base this. XCOM managed to capture the base with the Sectoid Commander and prevented potential EXALT operations, but over half their soldiers were killed with the rest wounded. Additionally, the Sectoid Commander managed to Mind Rape Twilight's presence from Matt's mind before it went down, and presumably transmitted her location to the Hive Mind.
In one chapter, Lana uses her cybernetic arm to karate-chop to effortlessly cave in a sectoid's skull, rather than use a knife like her comrades. However, in the ensuing gore, some bits of sectoid brain get stuck in her arm's joints, which Lana complains about.
In chapter 33 a frightened human mistakes Twilight's Unstoppable Rage for a threat and shoots her.
Shen is the first to realise that Twilight Sparkle acts absolutely nothing like the other invaders and to suggest a diplomatic approach.
Commander Bradford is also one; he agrees to allow Shen to try and make peaceful contact with Twilight, then supports his suggestions that they continue diplomacy. In chapter 8, he does point out that Vahlen's concerns are valid, but also notes that she will need to be reprimanded for her bullying approach to interaction with Twilight, something he does in chapter 11. He's also willing to give Twilight the benefit of the doubt while there's reasonable proof she is what she claims to be, and to try and make things comfortable for her without compromising the base. Shen himself says that so long as whatever you think of is logical, reasonable and beneficial, Bradford let you do what you want.
Red Shirt: Well, this is an X-Com crossover. Lots of soldier deaths is expected.
Twilight Sparkle has an invisibility spell and can also alter it to create an effect that drives people mad with desire.
In chapter 14, Twilight's attempt at using her translation spell on a Thin Man drives the normally stoic alien into a berserker state fuelled by hate so intense it mutilates itself to death in an effort to escape and get at her.
In chapter 15, the Council are constructing a new containment unit in the Argentina base specifically to hold Twilight Sparkle and, should Commander Bradford agree, she'll be sent there for... much more bluntly direct interrogation.
In chapter 28, because of Twilight's presence and her continued manipulation of the ambient mana, humans are gaining the ability to access it and becoming empowered themselves. As more people become empowered, they will make it even easier to access the Field, so empowerment will spread exponentially.
Roaring Rampage of Revenge: In his report for Supplemental Files 6, Dr. Frank McKendrick, the base psychiatrist, cautions X-Com to remove Lana and Matt from active duty and to avoid letting Twilight know that X-Com is even thinking of using her powers or knowledge for offensive purposes, lest she go on one of these.
Ron the Death Eater: Possibly due to Twilight's poor representations, the humans In-Universe are starting to wonder as of chapter 13 if Cadance may be the real biggest potential threat of the three princesses.
Sanity Slippage: In-Universe, several of the X-Com members wonder if Vahlen is perhaps going insane — she's been acting strangely, and refusing to see the base psychologist. Fortunately, once she has her Heel Realization, Vahlen gets much better.
Science Versus Magic: Averted. Alien technology turns out to be heavily based on melding science with magic, such as the "spell-circuits" (circuitry literally fashioned in the shape of runes and thusly channeling magic instead of electricity) that keep the slave-races obedient.
Shipper on Deck: Lana has all the subtlety of a wrecking ball when it comes to seeing Matt and Twilight get together, despite claiming she only started the idea to give Twilight something less major to stress over than her current tenuous position.
Ship Tease: Quite a bit between Twilight and Matt, dire circumstances and Lana notwithstanding.
Shoot the Bullet: In chapter 33 Zhang shoots an alien's rocket while it's still in the launcher.
The project names mentioned in chapter 26, while technically drawn from mythology, almost all also appeared in Fate/stay night. The "hit target before the projectile travels" guns from project "Gae Bolg" get the official designation of LANC.
Shut Up, Hannibal!: In chapter 34 Vahlen gets quite cross with a senior interceptor pilot who gives her lip about Twilight.
Shut Up, Kirk!: In chapter 20, Lana blows up when Matt and Shen call her out on shipping Matt and Twilight together.
Sixth Sense: Bradford apparently is really good at sensing people. When Lana was under the effects of Wallflower, he was the only man on the base who didn't fall under the Bystander Syndrome effects of the spell. It turns out it's because he's developing psionic powers of his own, namely precognition.
Sliding Scale of Idealism Versus Cynicism: The foundation of the story is the clash between two settings that exist on opposite ends of the scale. Even then, one can see both cynical and idealistic attitudes from the humans in regards Twilight.
Dr. Ngo postulates that Cutie Marks are deliberately manipulated by the adults to aid in social engineering, because she can't believe that they really are just abstract representations of natural talents or traits an individual pony has. She also suspects Princess Candance's empathic powers are used to help exert control over the ponies of Equestria, and, in a bit of In-UniverseFridge Horror, wonders just what Twilight's childhood was like growing up as a personal student of the effective queen of her world, with another princess acting as her foalsitter and eventually going out with her brother.
Shen postulates that Twilight makes friends so easily because she, passively or actively, projects a mind-influencing aura that induces people to like her and want to trust her. Despite this, he's still quite at ease around her, as he doesn't believe her intentions are hostile — she's trying to make them befriend her because she's in a very scary and threatening situation.
Dr. Frank McKendrick, the X-Com psychiatrist, is of the professional opinion that Twilight's "likeability" stems not from any manipulations on her part, but from natural human responses to her Adorkable attitude/behavior and appearance as a cute, cuddly, furry little animal.
Squishy Wizard: Twilight's spells are strong enough to destroy anything that XCOM can throw at her. On the other hand, XCOM doesn't really need much to take down Twilight herself. She was captured because she got hit by an Arc Thrower, and that only works on the aliens when they're nearly dead. Considering that Twilight wasn't hurt in the least when she arrived on Earth, that says something about her physical condition.
Stealth Pun: In chapter 35 Discord wears a black t-shirt with the XCOM emblem on it, with the words ‘That’s’ and ‘Baby!’ before and after the emblem.explanation In other words... That's XCOM, baby!
Super Toughness: In chapter 30, an EXALT trooper takes "a two second full auto burst in the chest" and still tries to get back up. Another one only stumbles after taking an Arc Grenade and Arc Thrower shot.
Taken for Granite: Used liberally during the XCOM Base Defense courtesy of Twilight against the Ethereals.
Talking the Monster to Death: In the bonus "What If?" chapter, Fluttershy uses The Stare on a Chryssalid to force it to bring them to the Ethereal Overlord, who she lectures until it seeks peace with Earth, and then she does the same with the Council of Nations. It's as silly as it sounds.
Tele-Frag: In chapter 33 Twilight does this to a Sectopod.
These Hooves Have Killed: Twilight seriously freaks upon splattering a Chryssalid, even though it was about to rip her apart, and is still shaken up by it in later chapters. In Supplemental Notes 3, Vahlen notes that Twilight absolutely refuses to use her "Crush" ability in the lab tests and instead breaks down and becomes hysterical at the idea. Just how hysterical is revealed in the next chapter.
Teleport Spam: In chapter 33 Twilight does a bewildering amount of this, taking down enemies all over XCOM HQ before heading to the surface.
They Would Cut You Up: Funnily enough, Twilight is already in the captivity of an organization where this trope is their typical MO. However, the Council has also recommended sending Twilight to another base where only painful experimentation awaits her, which many XCOM personnel recognize as a horrible possibility and seek to prevent it.
This Cannot Be!: In chapter 30 this is the Sectoid Commander's reaction to the XCOM troopers having magic/psionics.
Time Master: Discord is capable of this, turning a potential bloodbath into a scene of chaos while time was paused. He's even good enough to accelerate time on one specific object, specifically the homer's timer.
Vahlen... You have a subject who is quite obviously traumatized and blatantly freaking out at the idea of performing the task you want her to perform. This subject is also literally capable of killing you with a thought. Yet your approach is to continue forcefully pressuring her, driving her deeper and deeper into obvious hysteria, never once considering the fact she just might get so panicked she'll unthinkingly demonstrate her Crush power on you. Congratulations, Vahlen, you're a shoo-in for the Darwin Awards. Fortunately, Vahlen gets better.
Lana's teasing Matt over catching him hugging Twilight goes to the point that she puts a pinup portrait of Twilight in Matt's locker. As he promptly reminds her, anything relating to Twilight's existence is highly classified. If her superiors found out about it, Lana could wind up imprisoned or even executed for such an act.
In chapter 20, Shen's displeasure is demonstrated with a low-key darkening of expression, clenching of the jaw and narrowed eyes, compared to Matt's ranting, growling and gesturing.
Bradford in chapter 27 when Lana tries his patience.
Gone was the mask of sympathy and in its place was the glare that had made Bradford infamous. The one sentence he spoke filled the room more than Lana’s shouts even though it wasn’t a decibel louder than his usual speaking voice.
Translator Microbes: Twilight's translation spell. First used to communicate with the humans, chapter 14 sees X-Com try and use it to converse with a captured Thin Man. Results are... less than satisfactory.
Turn the Other Cheek: After Lana explains that Dr.s Ngo and Mills would not have put her into Interrogation had they been aware of who she is, and that Vahlen has her reasons for being so forceful about finding out how Twilight Sparkle can do things that defy the world as she understands it, Twilight readily forgives all three. Shen is amazed at Twilight's ability to forgive Vahlen, privately thinking to himself that he wouldn't in her hooves.
Unstoppable Rage: Twilight in chapter 33 after aliens kill Kim and Joel and critically wound Vahlen.
Commander Bradford gives one to both Matt, over his choosing to take part in mission Silent Rain despite his having an unknown "spell" cast on him by Twilight Sparkle, and to Vahlen, over her frankly suicidal attempts at intimidating cooperation from Twilight, in chapter 11.
Matt gets to give a similar speech to Lana over putting a photo of the highly classified alien lifeform whose existence she is sworn to keep secret under pain of imprisonment and/or death in his locker like a pinup photo.
Lana gets one from Matt and Shen alike in chapter 20 when she finally comes clean to them about how she tricked Twilight into thinking Matt has a crush on her.
Chapter 17. Vahlen finally breaks down and admits that Twilight really doesn't seem to have any sinister purposes, even admitting that Project: Stardust is a valuable resource in its own right. And Twilight receives a letter from her homeworld, meaning the Princesses have finally found her.
Chapter 20. Lana's "gag" comes out and leads to major strife between the members of Project Stardust. And Twilight has just figured out that Matt is the human who captured her...
Chapter 21. The Wallflower spell turns out to not work on the cybernetic alien forces, such as Cyberdisks. This results in Lana getting her arm shot off and then dying.
Chapter 22. Twilight has agreed to actively help X-Com defeat the alien invaders after learning some important details about how they work. She and Dr. Vahlen have discovered she can create "spell-circuits" using Elerium that will allow others to artificially replicate magic. Discord reveals he can see everything that's happening on Earth and reach out to its inhabitants at any time he wants... which he uses to bring Lana back to life.
Chapter 28. People are going to start developing psionic powers like wildfire because of Twilight's presence; the more people who "awaken", the faster it'll happen and the wider it will spread. Also, Twilight has been made known to the other Strike team leaders, who originally weren't in the know.
Chapter 32. What appears to be the Equestrian star system has been found. EXALT has slipped infiltrators into XCOM HQ and the aliens are beginning their attack on the base.
Chapter 33. The aliens attack XCOM HQ. Kim and Joel are dead, Vahlen is critically wounded, Twilight goes into Unstoppable Rage and wipes out most of the invaders only to be overpowered by the Overseer Ethereal and shot by a human.
Chapter 34. Twilight isn't getting better, so XCOM builds the "Kaleidoscope" to send her back to Equestria, only to be attacked by Luna and some guards and barely saved by Discord.
Chapter 36. War has come to Equestria, and the ponies are losing badly. The Ethereals have began assimilating them in a similar manner that they did with Exalt. X-COM soldiers are beginning to display more and more extreme abilities, and the Council has decided to aid the Equestrians.
Pinkie Pie's one-line letter to Twilight in Chapter 19
Pinkie Pie: Elerium!
The end of chapter 29.
Bradford: “Ladies and gentlemen, we have located the planet-side base of operations for the invaders."
With Great Power Comes Great Responsibility: Twilight's attitude towards some of her more extreme magic, like transmogrifying living beings or the Want-It, Need-It spell. She will not hear of performing such magic for X-Com, citing it as too dangerous.
Woolseyism: In-Universe; Twilight's translation spell works like this: Providing the best possible translation for whatever word she's saying to whomever she's speaking to.
Word Salad Title: Hilariously, the story offers and explanation for the ridiculous names missions would be generated with in XCOM: Enemy Unknown. Turns out they did have a machine that would just randomly match words together.
Twilight effortlessly crushes a Chryssalid... and is then taken down anti-climatically with one Arc Thrower shot.
Worf Had The Flu: In-Universe, it's noted that the soldier who captured Twilight had the luck of taking her by surprise, and her telekinetic powers means that an attempt to take her down when she's not stunned, confused and terrified would not be so easy. As chapter 33 proves. In spades.
In chapter 33 the Overseer Ethereal demonstrates its power by psionically immobilising Twilight with two words after the latter had run roughshod over its minions.
In the same chapter, after petrifying most of the invasion force, splattering a mechanoid with a vault door, and shooting down a scout and a battleship by ramming them into each other, she is taken down by a single pistol shot from a terrified fighter pilot.
You Were Trying Too Hard: Celestia and Luna grant Twilight her ascension to alicorn after the latter realises this of herself.
Mente Materia contains examples of:
And I Must Scream: Not content with the banishment instituted by Celestia (see Cruel Mercy below), Discord adds his own bit of horrifying: He lets the invaders' bodies burn on the Sun's surface. The original spell then restores them, only for the process to start again.
Cruel Mercy: Banishment to the sun is an And I Must Scream situation where the victims' bodies are kept in suspended animation but their minds are left free to think.
Downer Beginning: The first proper chapter - that is to say the second one - has a major alien attack on various Equestrian cities, including an Ethereal personally going after Twilight.
Eaten Alive: Discord eats a whole Muton Berserker in chapter two.
Eldritch Abomination: Discord, full stop. It was shown in Stardust, but becomes even more prominent in Mente Materia, with him eating a Muton Berserker (and half the street with him) in Chapter 2, and doing an Alucard-worthy multiple-eyes-stare to get information out of a guard in Chapter 3.
Mythology Gag: In chapter 3 one of the shell companies hiding XCOM is a PMC led by Otto X/Zander.
Oh Crap: Matt's reaction in chapter 3 to seeing Shining Armor on TV.
Person of Mass Destruction: Celestia and Luna amply demonstrate their sheer power in the second chapter. Luna destroys a... Battleship? ... with five magic beams in under a second and destroys its escorts with even greater ease while Celestia shuts down a small alien army and teleports away whole alien spacecraft while toying with an Ethereal and casually No Selling its attacks.
Restraining Bolt: Discord's curse prevents Celestia from physically harming any living being, which proves a hindrance even as she tries to bypass its limitations with spells that are only indirectly lethal.
Strawman Has a Point: Word of God states that the council is made up of unknown individuals, not representatives of funding nations. Senator Goleman's political attacks are completely justified as XCOM is a glorified PMC operating as it pleases, not an official multinational force. It has been pointed out that the nature of the Council is not completely known and they may take the form of The Illuminati, which means they not only control XCOM but the nations of the world as well. Strawman still does have a point, but not the one that he started with.