Abandoned Playground: There is a small patch of grass, with a swing hanging from the tree in the middle of it, in the middle of the abandoned arcology dome that Rei lives in. Notably, Shinji is Genre Savvy enough that he finds it creepy. Note that it looks almost exactly the same as Alma's Happy Place in Project Origin at Still Island. That can't be a coincidence....
Accidental Hero: Toja became one when he tried to find a missing Ill Girl during an evacuation of her school. A whole class of 10-year old girls ended up idolizing him for that.
Achilles' Heel: The joints of anyone with subdermal armor (which would necessarily include heels), whether NEG or Migou in origin, are less armored. Justified in that it is still necessary to move the joint, so of course they have to have less armor there, and it's still possible to kill them without hitting the weaker spot.
Averted with both the Nazzadi and the Deep Ones, as the former are basically just human, and the latter are still terrestrial creatures that use hemoglobin.
Alien Geometries: Everything related to the Harbingers, and especially so now that Mot showed up; think Rebuild 's version of Ramiel, only as a multi-dimensional combined fractal/polyhedron. Aeon War Syndrome, where the mind breaks trying to comprehend the seemingly impossible geometries, is a constant threat.
Alien Kudzu: The Leng ecosystem is a combination of this and an alternative set of laws of physics; the change to physical laws spreads in areas where it is permitted to grow, and it grows in areas where the laws of physics are different enough that it can survive.
Alike and Antithetical Adversaries: The non-human sides are debatable, but the NEG-led humanity is heterogenous. This is something the NEG is trying to change to a homogeneous society through various social programs so that they could get rid of various things that lead to internal conflicts.
Alternate History: At the start of Chapter 1, there is an excerpt from The Shadow Out of Time, which makes it clear that both the Elder Thing city in Antarctica and the Yithian city in Australia were historically discovered in the 1930s, putting the point of divergence quite a bit before now.
Word of God states that the discovery of the Elder Thing City shifted American interests out of isolationism; thus, the USA joined the League of Nations. Also, due to various political and military circumstances, the USA-Japanese war is considered almost completely separate from Europe's World War II; thus, the USA did not fight against Hitler until late 1942. This allowed him to use more resources against the USSR, prolonging the war to 1946, and Western allies nuked Berlin to prevent the Soviets from capturing it, thus making the foundations for two completly separate cities, Westberlin and Ostberlin.
Alternate Universe Fic: AEE is one to Evangelion and FEAR, while Cthulhu Tech gets the dubious honor of having everything be a point-of-divergence right after Vade Mecum because ES had declared everything post-Vade Mecumunsourcebooks.
Ancient Conspiracy: AHNUNG, who play part of SEELE's role. Oddly, the part of the Human Instrumentality Committee has been given to the Ashcroft Council of Representatives, who don't appear to be the same group (and, as a member, Gendo has quite a lot of influence on it).
And I Must Scream: The self-aware souls of the cats stuck in their physical bodies, with no way to control them or alter reality, like they're used to, after they were cut off from the Dreamlands.
Angry Guard Dog: Cybernetically modified and armoured ArcSec guard dogs with their shoulders reaching up to average man's waist, with the chips installed in their brain to be more alert. Toja's neighbor has a retired guard dog who is quite friendly, though.
An Offer You Can't Refuse: Gendo "recruited" Shinji with the threat that not joining the Evangelion project will result in removal of protection that keeps Shinji from the hands of various R&D departments...and their saws.
Arms Dealer: Ghouls were seen scavenging what was left over from the fight against Harbinger-3, and selling munitions to various parties, including Eldritch Society.
Artificial Gill: A variation with the "Eva EVA equipment", designed to keep the LCL in the body when exiting the entry plug in order to avoid complications of the sudden switching between breathing LCL and normal air when the normal supervised procedure is impossible.
Tank crews view mecha as this in-universe. They show their opinion by making sarcastic comments about stable firing platforms, optimized weight distributions, and low target profiles.
The narration states that Chicago-2, while awesome-looking, is simply outdated for the Aeon War.
Backpack Cannon: Unit-00 got jury-rigged with missile launchers on its back when delaying the blind Mot.
The Bait: Shinji's role against Asherah was to draw its attention while the conventional forces take it out. Maybe. And that seems to be a standard tactic now, after the incident in Chapter 4.
Balance of Power: The Aeon War is currently in the six-year-long relative stalemate with no major victories or losses since the Fall of China, which is close to collapsing since Mot appeared on the Eastern Front.
Beam Spam: Mot is apparently only capable of firing one beam from each face of its trapezoid form. But when it takes an almost gratuitous amount of abuse from the NEG, its response is to reshape itself into literally thousands of smaller trapezoids orbiting around each other - and each of them can fire a beam from their face. The resulting barrage of beams levels entire mountains.
Bigfoot, Sasquatch and Yeti: The real Migous, which are briefly mentioned to be a part of the Rapine Storm, are Yeti-like. The bugs in space are not actually Migou, but the name stuck.
Bio-Augmentation: Genefixing your unborn children to remove diseases and make them smarter or tougher was entering common use before the First Arcanotech War; it was heavily restricted after the end of the war (the fake Rubber Forehead Aliens didn't like it, on account of being created that way), and there are currently in-universe debates over relaxing the restrictions. Asuka inherited a heavy amount of augmentations from her mother, which is one of the reasons that she finds things so easy.
Bilingual Bonus: Quite apart from the puns or references often involved in the names of Ashcroft Groups and Projects, there is untranslated German poetry and Hindu scripture scattered throughout the story.
Black and Grey Morality: The NEG and the Ashcroft Foundation do some pretty not-nice things in the name of survival (and that's even before we get into the Evangelion and FEAR bits), such as weapons that kill souls, or make destructive neural maps of living people.
To be fair, the souls don't mean anything, if you're baseline human. Homo sapiens don't use them, and they don't convey any kind of immortality. For many of the NEG's opponents, though...
Blessed with Suck: The Sorcerers have the highest rates of cancer, and their children have a very high chance to get massive outsider taint.
Chapter 6 is unusually short and focuses on the rather cute and very curious 4-year old Asuka...a few days before her mother's scheduled Test with Unit-02. Ouch.
Chapter 11 is more of the interlude between chapters.
Chapter 13 is an epilogue to Rei-0X/Mot fight arc.
Bridge Bunnies: Ritsuko has lots of these. Unfortunately for her nerves, they tend to get into Tachikoma-like arguments.
Britain Is Only London: Most of England turned into one big city before the Arcologies were created. The Evangelion Project moved to London-2 after the Rapine Storm conquered China and got uncomfortably close to Japan.
The NEG-Migou conflict is the main example of this, although this trope is partially inverted, because the Migou are the more technologically advanced, intelligent, tool-users, and in fact have very little in common with traditional sci-fi "bugs" apart from their appearance.
The fight against the hatchlings of Harbinger-4, Eshmun, was a more conventional example of this trope, given that they were a bit insect-like, a bit squid-like, a bit crab-like, and had Combat Tentacles.
Buffy Speak: Sometimes, with Simon (the temporary therapist assigned to Shinji) being the most blatant example.
Cats Are Mean: Cats, as in the works of H.P. Lovecraft, are intelligent and don't really like humans. Much of this comes from the fact that they are now their pets, when in the past the humans were basically servitors with the task to take care of the cats' bodies, which the cats considered to be useless, since they spent almost all their time soul-surfing in the Dreamlands doing things incomprehensible to human minds. Then the Dreamlands were eaten, and now suddenly they are mere pets to former servants, while others had worse fates. Oh, and their eyes are used for security systems.
Cannon Fodder / Redshirt Army: For the most part the NEG Military is this as far as both the Evangelion Project and the Harbingers are concerned.
Cast from Hit Points: This is the side-effect of using sorcery, since it's like forcefully using the machine (human body and mind) for something that it was not designed for.
Chest Blaster: An improvised one, with the magically enhanced nuclear warhead placed inside a hole made by Mot in Unit-01's chest, just meters away from the Entry Plug. Spatial-distortion magic is used to ensure that the blast travels in a straight line as opposed to the normal behaviour of nuclear detonations..
Chekhov's Gun: Misato checking on a space-based project in chapter 4. In chapter 12, a nuke from that project was used to kill Mot.
Child Soldiers: This is Lampshaded and deconstructed, as might be expected. Project Evangelion is called on it by the Ashcroft Representative of Research, while the Representative of Ethics brushes over it. Shinji isn't too happy about it either, nor are Misato and Ritsuko. Neither is Asuka, but for entirely different reasons.
Chunky Salsa Rule: The Babylon Hypervelocity Rifle simply shreds the lesser Eshmun spawns.
The City Narrows: The Old London underground. The logistical and security nightmare that is a post-Harbinger battle cleanup certainly helps for those who wish to remain hidden.
Clipped Wing Angel: One-Winged Angel Mot, while still powerful, is structurally unstable and sacrificed its attack range for regeneration, which NEG uses to further delay it from reaching London-2.
Cloning Blues: When each of the main fusion series has this as one of the important plot devices...well, of course this is going to feature. However, unlike canon Cthulhu Tech, the Migou continued to make Nazzadi soldiers even after the defection, as reinforcements (and replacements) for the Loyalists, at least according to NEG Intelligence. (Because, really, how else could they produce that many soldiers?)
Collateral Angst: Toja's angst about failing to protect his sister is the main focus of that subplot, while his sister herself is rarely featured.
Competence Zone: Justified; it matches with real life. With the exceptions of Rei and Asuka, who were trained to pilot the EVAs from early age, everybody below 18 is about as competent as might be expected for their age, including Shinji, who survives because of raw talent, sheer luck and Unit-01's berserking. Everybody who is above 18 but not competent at what they're meant to do is an idiot, (about to go) crazy, or both.
Con Lang: Nazzadi appears to be an internally consistent language incorporating vocabulary from the Romance languages, but with a more Germanic grammatical structure.
Rei. In-universe, she creeps out Gendo, and he seems to be fond of her.
Critical Annoyance: They didn't had time to reprogram Unit-01's LITAN AI to ignore some modifications, namely the nuclear bomb in its chest.
Cryptic Conversation: Along with the whole prologue, pretty much all conversations that don't refer to immediate events (and sometimes those too) can be extremely cryptic.
Culture Clash: This leads to various issues regarding the Nazzadi and Xenomixes, especially in mixed families. There are also issues with the Nazzadi and Xenomixed among the older generation, to whom they're immediately associated with an unwinnable war.
Asherah, the re-skinned Sachiel, owning everything that NEG throws at it...and being smug about it.
Earth Scorpion: Seriously. Sachiel is up there with Ramiel and Zeruel for destructive power. It's just that because it's the first to appear, that it tends to go down like a bitch in fanfics.
The introduction of Asuka and Unit-02 is pretty much this. The music it is set to is appropriately named.
Cybernetics Eat Your Soul: Blanks are made by creating a secondary artificial neural network in captured humans and xenomixes. Notably, this trope name is literally false; the presence of a soul is something which can be quantified.
Cyborg: The Military personnel are modified for war, starting with eye modifications as noted below, to serious modifications that fighter pilots undergo in order to be able to compete with the Migou air force.
Deadpan Snarker: Almost every character shows some elements of this, most notably Shinji.
Designer Babies: The first Nazzadi were this. Continued by the Migou with the new-and-improved and most importantly loyal elite loyalist Nazzadi.
Desolation Shot: Old London. Steadily getting more desolate, too, it should be noted, even before the collateral damage from the Harbingers is taken into account.
The Determinator: Gendo, as seen during the Unit 00 incident, is one. Likewise, throughout the entire Harbinger-3 incident, he was on just enough painkillers to allow him to think through the pain of his hands, without showing any sign of discomfort.
Didn't See That Coming: Discussed in Chapter 10. When the TITAN is reporting what is known about Mot, Misato remarks that at least they knew the Known Unknowns.
Discontinuity Nod: It is noted that, in-universe, the Nephilim technology evolved from the useless Mortal Remains-style leash dogs (who are also nearly-guaranteed to go out of control and will always try to kill their handler first) to, among other models, the spider-like Tsuchigomos (which put the squishy human pilot inside a safe armour-plated pod, and are more like mini-Engels). The Loyalist Nazzadi seems to be a nod to the elf-life Nazzadi of the canon Cthulhu Tech.
Easy Logistics: Averted in general. It's also the reason why the NEG can't use strategic conventional nukes as mines against Mot again and why Unit-02 won't be in time transferring from Chicago to Europe.
Those who serve in the military are offered to replace their organic eyes with artificial ones (or harcontacts, hard permanent contact lenses, for those who refuse) due to things on the battlefield, mostly lasers, that tend to fry the eyeballs just by looking at them.
Asuka apparently lost her organic eyes due to looking at a nuclear detonation.
Loyalist Nazzadi come in an Elite variety, who have extensive cybernetic and genetic enhancements, and are issued Migou-level weaponry and gear.
Combat Blanks, reprogrammed humans, are more akin to a light suit of power armor even before they have equipment, and have small antimatter reaction chambers where their guts would be which are used to fuel their integrated weapons and enhancements.
Epigraph: Every chapter starts with one. Some of the quotes have been appropriated from real-life sources, while others are thinly veiled Infodumps.
Everything's Better with Penguins: This Pen-Pen is a Antarctican Urbanised Albino Emperor Penguin, which means that he's descended from the giant albino penguins in At the Mountains of Madness, resident in the Elder Thing city.
Everything Is Online: Averted. Since the Migou are the masters of hacking, the Grid is heavily protected, segmented into regional parts, and contact between them is allowed only at specific times through specific heavily monitored channels.
Gendo has one. In fact, he practices sorcery in a tower, which looks over a city, which is in a hidden cavern underneath another city composed largely of pyramidalarcologies. That man has serious style.
Mot transformed itself into the spire that kept extending both upwards and downwards in order to get inside the Geofront. After it was killed, Mot left behind a kilometer-tall spire-corpse for Ashcroft to clean up.
Eye Scream: Hollow socket variant with Rei. In the battle against Asherah, it rips Unit 01's eye out with lamprey-like hands.
Failsafe Failure: Averted; most of the failsafe failures were the results of said failsafes being damaged or destroyed. Asuka complained on how they screwed things up when dealing with Subsystem Damage, though.
False Flag Operation: As done by the Migou operative in Chapter 7 to kill a senior NEG Army officer.
Fictional Document: Excerpts used as epigraphs for chapters and the diary from Chapter 14.
Firing One-Handed: Subverted, as firing the Eva-scale Babylon rifle one-handed is a sure way to damage the Eva's arm, and hurt your own hand (and slap yourself in the face). Then again, one of Unit 01's arms was already crippled, so he didn't have much choice.
Fiery Coverup: Asherah and the NEGA pretty much destroyed most of the clues and evidence of the unidentified agents in the airport by fighting each other (well, the former pwning the latter to be more accurate).
Flanderization: In-universe, Theresa Ashcroft is treated as the sole inventor of arcanotechnology, while she was actually just the first to combine the various inaccuracies in the Standard Model and Quantum Mechanics into a single scientific field.
Foregone Conclusion: It's a rewrite of an ElseworldsFusion Fic following the canon storyline of a TV series set in a Mythos universe. The exact details are unknown, but details have a nasty tendency to drive people mad.
Homeschooled Kids / Corruption of a Minor: NEG has forbidden homeschooling on the basis that cultists would use it to their advantage, basically legally training the next-generation of cultists. Played with when Shinji complains that the high brass made him go to school when homeschooling would be much more efficient in his case, considering that breaking the no-homeschooling law is nothing compared to him being drafted as a Child Soldier.
Huge Holographic Head: Gendo does this in the Father/Son reunion scene, although it's actually just rendered onto Shinji's Augmented Reality-glasses.
Human Aliens: The Nazzadi are so human compared to the other sentient beings that you will forget that they were aliens in the first place, especially the younger generation. Because...well, genetically, they're an artificially-created Human Subspecies.
Humans Are Morons: How almost everybody non-human views humanity in general and the NEG in particular. This view is especially held by the Migou (and Earth Scorpion).
Humans Are Special: Subverted. We're an species descended from out-of-control Elder Thing hypertech on a world which is important because it's claimed by much more powerful species than us, and we're the idiots mucking around with technology we don't understand.
Human Shield: A Blank swiftly uses a captured medic to protect herself from enemy fire. NEG soldiers are trained to ignore human hostages.
Ill Girl: Imi, the girl who Toja ran out to try to rescue (and one of his sister's friends), was looking for her medicine. Toja's sister and Rei are also examples, but Rei is Rei.
Inertial Dampening: Aircraft pilots are heavily modified with cybernetics so that they could tolerate high Gs in order to compete with their Migou counterparts...and they still can't cope with Misato's driving.
Instant Death Radius: Mot is a Ramiel expy, so it's a given. It gets a little bit more literal after the NEG's initial assault.
Invisibility: One of DAEVA's (now rechristened as DAHACA) selling points.
Irony: Director Khoury (named after the parents who never existed in the first place), a Nazzadi ex-soldier serving on the invasion fleet (which has no real history), currently holding a position of Director of Secret Services (which officially does not exist).
Jaw Breaker: Asuka rips off Yam's jaw while falling down from near-orbit.
Jerkass: A mild version with Ritsuko, who unlike in canon doesn't act nice, and is usually blatantly unemphatic, but she is so consistent about it that she comes off as less of jerkass she was in later parts of Neon Genesis Evangelion, and as more of a person who tries to cope with her job that has a very real (and inevitable) risk of being driven to insanity.
Jigsaw Puzzle Plot: ...with just about the right ratio of answers to new questions. Note that unlike the fic's source material, the picture the pieces make when put together actually makes sense...appropriately, in a very horrifying, Lovecraftian sort of way. Also, even knowing what the hell was going on in Evangelion won't help you much here.
Layman's Terms: Common, both in narration and by characters, usually Misato telling Ritsuko to repeat something, only in human language (figuratively).
LEGO Genetics: Averted. Gene fixing is a very complicated process with its own share of problems, like a genetically-enhanced math genius being unable to recognize faces, including her own in the mirror.
Les Collaborateurs: The Migou "cultists", who work for the Migou out of their own will. They're dangerous because, by and large, they're not cultists in the Lovecraftian sense. They may be fanatically devoted to the Migou, but within that frame of reference, their actions are fully sane.
Let no Crisis Go to Waste: A lot of people use the chaos caused by the Harbingers showing up (and the immediate aftermath) to further their own goals.
Little Hero, Big War: As important as the Evangelions and the Harbingers are, the Aeon War doesn't revolve around them.
Lockdown: Heavy quarantine on the Budapest-infected locations. Certain specialists were sent to deal with it.
Lost Colony: The Nazzadi fake memories have Earth as one of the renegade colonies as a result of slower-that-light travel.
Losing Your Head and Helping Hands: The nervous system of the Combat Blanks (brainwashed, enhanced people) is modified to be autonomous, to the point where getting shot in the head won't stop them and severed limbs are still under their control.
Mind Probe: Used as a standard technique by the OIS. There is even comparative discussion by OIS agents on the ease of probing dead brains (and how decomposition affects the procedure) as compared to live ones.
Mockumentary: Instructional Lessons For the Youth of Today and Stuff, the TV show that Misato watches in Chapter 4, is styled like one.
Mobile Maze: Implied to be one of the security measures under London-2. Misato still got lost even though it was off.
Mohs Scale of Science Fiction Hardness: A definite 2 — there's plenty of physics-breaking to go around, but it's all explained and internally consistent. Like most good 2s on the scale, it reads as if it were far harder than it actually is.
The Mole: Besides the Infiltrator Blanks, there are also willing followers who truly believe that surrendering to the Migou is a good idea.
"They held their posts at the whim of the Senate and the President, they were not democratically elected, and they were technically speaking, nothing more than advisors. And if you believed that, then you might be interested in purchasing some prime real estate in Tibet."
Shinji thinking himself to be better than the prince in the fairy tale "Snow White" (Shinji was familiar with the original, NSFW version.)
When Shinji is learing to properly pilot Unit-01, it sports the original purple/green paintjob specifically made for testing purposes.
The show Misato was watching in ch. 4 ruthlessly (and hilariously) deconstructs Evangelion's "hedgehog dilemma" theme.
A medic dies not long after he is introduced. His name is Marek Janckowski.
After being submerged in blue LCL used in what may have been the memory-backing up procedure, Rei's hair was temporarily dyed blue.
The "recreation area" where Rei lives is a ten by ten patch of grass with a tree (trans)planted in it, with a swing on it.
As both the Evangelion and Engel Projects are researching the corpse of Eshmun, a doctor from the Engel Project said that they have codenamed the Engel design based off its offspring "Shamshel".
My Significance Sense Is Tingling: Harbinger-based Aeon War Syndrome usually does this region-wide, with Mot's presence making various sensitive people go crazy, and the Children seems to have more "natural" version of this when Harbingers are about to show up.
No Transhumanism Allowed: Like in Cthulhu Tech, thanks to Nazzadi leaders any research into anything transhuman was stopped (at least officially). Unlike in Cthulhu Tech, the influence of those old Nazzadi leaders is starting to fade.
Nothing Is Scarier: In Chapter 17 when Asuka used the camera feeds to figure out the situation with the Harbinger attack, she finds out that the Harbinger was nowhere in sight and that everything was way too calm.
Nuclear Option: Arcanochromatic nukes. Not used because of the risk of possible Migou response with strategic orbital bombardment. Conventional nukes are fair play, though, as the...
Nuclear Weapons Taboo: ...is thoroughly, thoroughly averted from the source material. Although the nuclear weapons used aren't (always) conventional ones, that's just because the use of variant r-state electrons (which act like muons) make the reaction easier to achieve, to the extent that tanks can fire small nukes. Which leads to...
Nuke 'em : ...as a standard response. Harbinger-5, Mot, is hit by a 12 megatonne pure fusion device, to soften it up, before the Evas and the Navy attack from long range. It doesn't go as planned.
Nuclear weapons are then used against it again, in the form of a nuclear warhead mounted inside Unit-01's chest, with spacetimed warped so that all directions point away from the Eva. For once, it actually works.
One Side of the Story: After reviewing the Harbinger-4 battle, Asuka criticizes Shinji's dismal performance under the assumption that he also had at least had 8 years of training.
One Steve Limit: Averted. Shinji's foster little sister is named Hikary. Considering the number of people named either Hikari/y or Horaki in ANE, Earth Scorpion is probably doing it on purpose.
One-Winged Angel: Mot, going from the equivalent of Series!Ramiel to Rebuild!Ramiel.
One World Order: Word of God says that the NEG (or at least the Unionist, rather than Federalist parts of it) is trying to systematically, and slowly, lessen the difference between the the former nations that make it up, with the goal of both sanitising the culture of harmful (like, say, Cthulhu-worshipping) influences, and preventing internal division which might weaken it. The NEG has explicitly been called a proto-Interim Coalition of Mankind, which is to say, like a secular, efficent Imperium of Man.
The Only One: Averted; everybody who are expected to be competent at their jobs will be competent. There is a little of this trope with Asuka, who feels that most of the higher ups are compromising her piloting, though she knows better.
Operation Xerxes, a More Dakka plan against Harbinger-4.
Operation Ankou, Nuke 'em plan against Harbinger-5.
Our Gods Are Greater: Now renamed to Harbingers, with the term Herald being a supercategory for the former.
Our Souls Are Different: For humans and their derivatives (or, at least, baseline humans), souls are useless evolutionary baggage that come from being Shoggoth-descended. That's an anomaly; most creatures, like the Migou, use their souls (which is to say, higher dimensional parts of their body) to think. Shoggoths are meant to, but Earth-life is broken, and, against design, has managed to evolve sentience, then sapience, only using three dimensions. Parapsychics and sorcerers tap into this heritage to fuel their powers.
Outgrown Such Silly Superstitions: Averted. While weakened, organized religion still exists and fares well. Some also proclaim that the empirical "soul" discovered by science is different from the spiritual soul.
Overheating: Asuka does this deliberately so that Unit-02 won't freeze in the water.
Played with when Misato suspects that Shinji, being Gendo's son, might be masterfully hiding his true intentions behind the mask of normalcy, until dismissing it as paranoia on her part.
The almost undetectable Blanked Infiltrators are this for the NEG military.
Pastiche: Chapter 14. One massive Lovecraft-homage, written in his style. And then finished by a preview where Misato promises more Fanservice in Book II.
Path of Inspiration: Played with, for the Nazzadi religion/philosophy. It was fabricated by the Migou to maximize their efficiency, and also designed to be cult-resistant by encouraging people to be open with each other; the thing is that it works, to the extent that some humans have begun to practice it, too.
People Jars: The medical variation with Rei inside and then Shinji.
Phlebotinum Analogy: When Ritsuko explains what they found out researching Eshmun's corpse to Misato, the latter mentions "classical" waves and particles. This annoyed Ritsuko.
Pistol-Whipping: Xuan Do beats the Infiltrator Blank with the butt of her rifle.
Playing Possum: What a Migou cultist ends up doing in Chapter 7, completely by accident.
Point Defenseless: Averted. Those laser point-defense systems on the Evangelions are good at their jobs.
Poisoned Weapons: Poisoned tiny hair-like carbon-fibre syringes are used by a Migou agent to assassinate a Marshal.
Powder Keg Crowd: The people at the airport panicked; some fled, some attacked the police. Of course, the fact that Harbinger-3 was currently attacking might have had something to do with how volatile they were. And the OIS sub-storyline seems to suggest that it was an arranged cover for some other group.
Precocious Crush: Toja got himself at least one such crush from a 9-year old (or a whole class of them, depending on how you interpret the scene) because he tried to save one of his sister's classmates.
Prophetic Fallacy: Implied when Mot shows sooner than expected, not to mention more powerful than expected. As of Chapter 18 this is questioned even further.
Proud Warrior Race Guy: The Loyalist Nazzadi, though the new Elite dropped this. Some of the Traditionalist families are also like this.
Pun: "Eva EVA equipment"; it got a chuckle out of Ritsuko.
Purple Prose: Avoids the usual shortcomings associated with this style...most of the time.
Pyrrhic Victory: Yam is killed, but Chicago-2, the capital of NEG, is a flooded, unrecoverable mess, with millions of casualties. Three of the Ashcroft board of representatives who were in the capital are killed. And more personally, Asuka's first official Harbinger kill will be forever overshadowed by the above.
Race Lift: Several characters were Type-1 uplifted to Nazzadi or xenomixes, to represent the demographics of the setting.
Rapid Aging: Involved in Project Herkunft Replica training.
Reality Ensues: If one concept defines Aeon Entelechy Evangelion, it's this. Insofar as reality applies in a setting with sorcery and lobotomized god-monsters, it has a tendency to rise from the depths, roaring, and slide its tentacles into any scene from the source material that it can.
Real Robot: The non-Eva mechas are this, and the Evas themselves are more closer to this when the AT-Fields are not involved. In fact, this appears to be a setting element; Asuka criticizes Shinji for failing to use Unit 01's AT-Field to get away with firing the Babylon one-handedly, with a strong implication that she could do it.
Reality Warper: The AT-Fields, and anything with the ability to produce one.
Ritual Magic: Imported from Cthulhu Tech, this is the only type of magic humanity can use. Used to revive Shinji.
The Roaring Twenties: The events described in the Chapter 14 Diary take place in the post-WWI Germany.
Robot War: The execution of Operation Xerxes is heavily coordinated by TITAN AI network; something that the NEG military normally restricts more, due to the threat of Migou hacking. It has also been stated that a lot of vehicles feature the human crew monitoring and guiding the Limited AI systems that actually control them.
Scenery Porn: Chapter 5 has higher dimensional non-Euclidean scenery porn, where detail is lovingly lavished over a metaphorical description of the higher dimensions close to Earth.
Secret Test of Character: Calvin likes to make these for Asuka, to the point that Asuka is almost starting to think that all of her interactions with "Uncle Cal" are these.
Self-Destruct Mechanism: The Migou biologically dissolve very fast, seemingly as a part of this trope. The Combat Blanks also explode upon death, and the Migou used infiltrator-Blanks with implanted antimatter capsules to decapitate the North American NEG command.
Shaping Your Attacks: Making the nuke explode in one specific direction without destroying everything else, like the Evangelion where said nuke is housed.
Sliding Scale of Robot Intelligence: Various, starting with dumb LAIs, moving up to muses, a form of personal assistant programme, and ending with TITAN networks, although nobody has a idea of the latter's level of sapience or if it even exists.
While waking up Cthulhu is probably the worst thing that can happen to everybody, on their own the Esoteric Order of Dagon is the weakest player in the Aeon War. Their resources and manpower are limited, and the only reason they aren't wiped out is that the big boys of Aeon War are too busy killing each other.
After their initial success in China, the Rapine Storm progress was halted and the new quarantine measures (the no-man's overkilling zone) nearly guarantees that no Storm army will pass, and due to their insanity they keep wasting resources trying and failing to breach the quarantine.
The Children of Chaos (Nyarlathotep) and Death Shadows (Hastur) cults. Their goal is to subvert humanity from the inside, and even with the NEG's infamously strong security, these guys keep finding holes in it.
The Migou are the main enemies of humanity. They have enough firepower to easily defeat NEG and bomb humanity to the stone age. The reason they haven't done that already is that they are afraid of waking up something worse in the process.
The Migou successfully conquered most of northern parts of North America thanks to the infiltrator blank with a built-in anti-matter bomb that killed most of regional command stationed in Alaska just as the attack started. Since then, NEG security has become even tighter.
In chapter 12, this happens during the Mot fight, with the bombs that were set up during the evacuation chaos earlier.
Spider Tank: The Tsuchigumo model of Nephilim, a kind of lobotomised Eldritch Abomination based on a spin-off from the original Evangelion Project, are rather arachnid.
Spoiled Brat: According to Hikary, most of the school is like this as a result of them being children of Ashcroft elite. She also claims that it's averted with the Horaki sisters, where their father made sure that they understood that being a part of Ashcroft elite is no reason to be become snotty. Of course, she might be an Unreliable Narrator for that...
Spy Satellites: A few remaining satellites that were not shot down by the Migou. Their usefulness is hindered by Migou's orbital superiority.
Square/Cube Law: One of the points the author mercilessly lampshades on when the Mechas are present, EVAs included.
Summoning Ritual: One asylum prisoner tried to make a summoning circle under the influence of Mot before being restrained. One of the military suggested that Mot is a result of Migou's botched summoning.
Super Prototype: The Evangelions to Engels, in the sense that the Cray supercomputer was a prototype for a gaming desktop. From a strategic standpoint against conventional enemies like the Migou, the Eva aren't worth very much either, as the Engels can be mass-produced and don't require Child Soldiers as pilots. From a tactical standpoint, on the other hand, an Evangelion will tear a formation of Nazzadi Loyalists a new one. On the other hand, from a strategic standpoint against enemies like the Harbingers, the Evas are indispensable.
Technology Porn: The technologies used in the story tend to get explained, even when they're using purely fictional laws of physics to operate, and, of course, certain things (like, say, the Total Information Tactical Analysis Networks) get rather loving descriptions of their operating principles.
Thememobile: Ritsuko at one point calls Misato's car "Misatomobile." Misato is not amused.
Theme Naming: The Space-Combat Project has a spear theme, with the facility in Germany named after one of three divine spears of Japan.
There Are No Therapists: Averted, thanks to the story's Cthulhu Tech heritage. Shinji is actually subjected to mandatory counseling, to prevent him from going crazy.
Tracking Device: A few of the spikes Asuka fired at Yam have tracking devices in them, tagging it so they could track in the murky waters.
Translation Convention: Averted with the sections of untranslated Nazzadi language. However, you can normally work out the meaning from the context, and some fans have tried to build a basic translation guide.
Viewers Are Geniuses: Hey, guys, let's spend a paragraph or two explaining how what the Harbinger is about to do is impossible, before it does it anyway. And, of course, the author much prefers implication to actually stating plot elements (while loving to Infodump on technological matters).
We Will Have Perfect Health in the Future: Courtesy of Genefixing. Except for those who get the short end of the stick by having side-effects caused by said genefixing, like Imi who is in constant pain and has to use painkillers.