Adaptational Badass: Kotohime. In her short canon appearance, she was an insane princess who thought she was a police officer. Now? She's a police officer who was able to arrest Marisa freaking Kirisame. Granted, Kotohime was having a very, very bad day. And she had Yukari helping her.
All Stories Are Real Somewhere: After The Reveal, Yuuka wonders whether the universe she lives in is real or just a fantasy inside the writer's mind, or if all the alternate universe she has seen exist or not. So far, this hasn't been neither confirmed nor denied.
Almighty Janitor: Genji is implied to be this. We still don't know to what extent, though, but he's apparently older and more powerful than Yukari.
Ambiguous Innocence: Yuyuko acts rather childlike frequently, not seeming to understand that things like eating Mystia and forcing her to remain alive throughout entire process are wrong. Her Obfuscating Stupidity makes this even more ambiguous.
Author Avatar: Yuuka, after The Storm arc is this, in a very twisted way. She lampshades and discusses it herself. It's very easy to compare how she makes other people suffer for no apparent reason with how the author hits the characters with every kind of calamities for the enjoyment of the readers. Or the fact that she constantly seeks to breed conflict. And we all know that without conflict, there is no story.
Chandler's Law: In chapter 39, right after the fight between the Strutter and the Hisoutensoku has been ended and Reimu is trying to convince Rin Satsuki that she's there to help her, Yuuka lets Tenshi pass through the crowd control and later helps her recover from the missile that Mima shot to her, and later uses the Strutter to challenge Reimu and her team. Why? For shits and giggles, of course. TakerFoxx himself admits to using her to get the plot moving.
Character Development: Reimu, much to her displeasure, is forced to admit that she's becoming more of a "people person".
Continuity Nod: Chapter 24 has one to A Very Nineball Christmas. When Yuuka takes Team Nineball to her mansion, Daiyousei's snowglobe is among their possessions that Yuuka has brought over.
Cool Sword: Reisen eventually finds Ex-Rumia's sword. It's described as obsidian black, with nasty-looking blades sticking out of everywhere.
Could Have Avoided This Plot: The incident that triggered the chain of events could have been mitigated, even resolved, if the characters had invoked the spellcard rules. Justifiable, though: one can't expect the Shadow Youkai to follow the rules.
Most of Gensokyo'spowerhouses join together near the beginning of the story to take down Rin Satsuki. It doesn't end well.
Satori literally gets curbstomped by Yuuka during Yukari's attempt to permanently get rid of her.
Cute and Psycho: Yuuka smiles almost constantly, and most of the time is almost pleasant to be around. Then she kills people because they happened to be in the wrong place at the wrong time, were in her way, or just to make a point. She used to be a lot worse about this: Yukari said she'd murder whole villages because she'd think it'd be funny.
Dark and Troubled Past: Elly. When being taken in by Yuuka is the best thing that has ever happened to you, something's gone very, very wrong with your life.
Deader Than Dead: The Kirin have access to a way of killing youkai and faeries and keeping them dead. They did this to Rin's biological parents as punishment for the scandal and treachery they performed.
Yukari is also capable of this, by crushing a being's 'essence'. This causes the target to be incapable of reforming its body. Yuuka walks it off.
The influence of Mykr's Sirens can prevent a youkai or divinity from regenerating from bodily disruption if there's enough of them around. Fortunately they'll come back once the Sirens have been weeded out. In ch. 39, this is the only hope for Kanako and Nitori.
Disproportionate Retribution/Wicked Cultured: Yuuka, despite everyone in-universe saying she's unpredictable, has a method to her madness. She only lashes out when someone breaks etiquette. An example being when she killed the couple in the hotel room, because they screamed in terror upon seeing her instead of giving her a proper greeting. Another example being that she didn't attack any of Yukari's backup teams until they attacked her, thus breaking the rules of her engagement with Yukari.
Kanako picks up on this and manages to talk Yuuka into going home for the day.
Dumb Is Good: Utsuho, very childlike and naive but also the only character to befriend Flandre, and go offer condolences to Remilia (who had been rather abrasive towards her) after Flandre's death/capture.
Eldritch Abomination: Yuuka is a (former?) Outer God, and her true form seems to be a flower described by H. P. Lovecraft out in space, going everywhere. Satori saw it, which caused her to blank out. Later, Yuuka explains to a guest that what Satori actually saw was but a watered-down version of Yuuka's true horrific visage, and at the height of her power, she was even nastier.
Eloquent In Her Native Tongue: Whereas the Kappa normally speak with an accent appearing to be a bizarre fusion of Jamaican and Dutch, the conversation between Sanae and Nitori in the Kappa's language displays a ridiculous level of articulation.
Fangirl: Patchouli was incredibly eager to meet Mima, having read all her books, and obsessively studied all of her theories.
In Ch. 38, Sanae is utterly unwilling to let Reimu try to stop the scuffle between the Strutter and the Hisoutensoku, or move from her vantage point. Why? It's a MECHA FIGHT!!! Then, when she gets to commandeer the Hisoutensoku in Ch. 40, she convinces Mima to let the main theme to Tengen Toppa Gurren Lagann play in the control space. So it's only natural that she finishes off the Strutter in ch. 41 with a Giga Drill Breaker.
Fantastic Nature Reserve: In chapter 39, Mima implies that Gensokyo is not the only Fantastic Nature Reserve in the world: there seem to be others for other mythologies. Seeing how it has already been made clear that in the Imperfect Metamorphosis universe both the Judeo-Christian God and Lovecraftian Outer Gods exist, it seems likely that these reserves really exist.
Confirmed in chapter 42: apparently they were created when YHWH took over and offered to let the old deities live if they agreed to stay there.
Fantastic Racism: Nearly every denizen of the Human Village has this with youkai. They shun Reimu despite her being one of their few protectors because she's friends with youkai (as opposed to, in Touhou, simply not acknowledging her efforts). They shun the GPF despite them being the first organised law enforcement agency in Gensokyo's history because they also protect youkai. And Master Sonozika outright hates youkai, especially Yukari, and anyone who associates with them under a fairly standard "all youkai are the same" mentality.
Forbidden Zone: The Garden of the Sun (which, in canon, is populated by fairies who help the garden grow by pointing them towards the sun) and a city that was nuked to Hell and back by Yukari are considered like this.
Foregone Conclusion: The plan to kill Yuuka is being told by Yuuka herself. This is being told after the actual attempt itself.
The four chapters of The Storm are basically a simple situation —a battle— which rapidly degrades. The results and the full implications of this battle are downright impressive: Satori was mind raped, killed by Yuuka and sealed in her team's crystal, Flandre was mentally tormented by Yuuka before being killed and sealed too, Sakuya and Remilia are terribly wounded and depressed, Yuuka is an Outer God and she learned about other dimensions, Yukari's soul has been corrupted...
Gambit Pileup: Everyone wants to use the Shadow Youkai to their advantage, or destroy it, or somehow save face in front of everyone else. Just try to count all the different plots, gambits, and motives running in this story. And it's not over yet.
Get A Hold Of Yourself Man: Patchouli does this to Remilia in chapter 38 to snap out the latter of her grief over Flandre's capture at the hands of Yuuka
According to Word Of God, YHWH is not a case of God Is Evil or Jerkass Gods and he was placed more to provide a backstory for the Shadow Youkai. It also must be considered that only Yukari and others with equally negative opinion of YHWH manifested their opinion on him.
Most of what Eirin has done as seen by herself. A defense program that she was involved in while still on the moon created a nearly indestructible monster species that got loose and continued to terrorize the Lunar Capital to this day. Kaguya, upon drinking the Hourai Elixer, was supposed to bring fame and fortune to both herself and Eirin, but instead was disowned and banished to Earth because if it. Rin Satsuki is just the latest on a long list.
And she already had one of this moment in the end of The Storm, when she learns she's fictional. See Mind Rape below.
Humongous Mecha: Two of them—the Asakura sisters' Strutter and Nitori's refurbished Hisentensoku—battle it out for the rights to capture Rin. It ends in a draw—piledriving the Strutter caused too much wear to the Hisentensoku's legs.
Idiot Ball: Reimu gets the bright idea that she can talk Rin Satsuki into compliance, or at least more willing to accept help. Rin Satsuki's paranoia and madness, unfortunately, just make things worse, forcing Mima to save Reimu. TakerFoxx openly admits that he's doesn't usually like this Trope unless they are well written.
Villain Ball: Telling Yukari how you learned of her assassination plan? Really, Yuuka? Really?
The reason why Yuuka joined the fray, combined with Worthy Opponent and thinly-veiled lust for Team Nineball.
Mima's justification for helping in Reimu. Interestingly enough, the "it" in question is not Rin Satsuki, as was initially apparent, but rather Reisen's ability to act as an Unwitting Instigator of Doom.
It's All My Fault: Reisen's self-esteem was quite low to begin with, but after Mima's rather cruel Hannibal Lecture, she snaps in chapter 45. Luckily, Byakuren is always ready to help her get a grip on herself.
Jerkass: A lot of people took a level in jerkass in this fic.
Mad Scientist Eirin, who constantly treats Reisen like shit, even after fucking up her adopted daughter for minor trivialities, and quickly starts arguments over who's responsible for Ex-Rumia. Reisen calls her out on it at one point.
Journey to the Center of the Mind: Rumia had done this in the Deep Within chapters. Kaguya, Mokou and the Shadow Youkai are doing their own one in IM: Rhapsody of Subconscious Desire.
Karma Houdini: Mima is a prime example: despite everything she's done, she is still free and hasn't suffered any consequence whatsoever. She even lampshaded it herself.
Another example would be Sakuya, Patchouli, the Asakura sisters and especially Eirin. While the Asakura sisters later in the story are on the receiving end of a Butt Monkey treatment, Sakuya and Patchouli not only do not suffer any consequence whatsoever, they don't even show the least hint of remorse for what they've done, apparently not caring in the slightest about the fact that they basically condemned an innocent child to a Fate Worse Than Death. Eirin also seems this, at first, but her case it's a bit of a subversion. Yes, she never gets called out on it, despite her being the one most involved with the Satsuki experiment, but it's shown at a point in the story that she's been consumed by remorse for all the nine years after the incident, and has never stopped trying to find a cure to undo Rin's transformation. It's actually a very humanizing moment.
Kill the Cutie: Subverted, but still a reader punch. Yuuka pierces Flandre's heart with a wood stake. Thanks to Youkai Immortality, there is her essence left. And then, Yuuka seals her.
Knight in Sour Armor: Byakuren knows that her ideals won't be quite achievable, not to mention how the rest of Gensokyo lives, yet, she doesn't renounce her ideals, living by them while accepting reality,however, she is one of the more polite examples.
Reimu is a more classic exemple: she is definitely more jaded and cynical than Byakuren, and keeps a cold and harsh fašade (at least initially), but after Reisen asked her to help Rin, she finds out that she simply can't stand on the sidelines watching while everyone tries to kill Rin because they think she's too dangerous to be let alive. This is also lampshaded often by Marisa:
Marisa: "But still. You do have a really bad hero complex. Sure, you bitch up a storm every time you gotta go outta your way to help someone, but you still do it, ze. It's who you are."
Kick the Son of a Bitch: Remilia beating Patchouli and Sakuya could be seen as this. Even if she didn't exactly do it for noble reasons (she was more upset about the fact that they agreed to keep Rin in her house without telling her anything than the fact that the two took part in Eirin's experiment), they really deserved it. Also, the Butt Monkey treatment that Mima or Yuuka inflict on the Asakura sisters.
Laser-Guided Karma: The tarantula youkai who harasses Cirno and gets frozen for it in chapter 4 had previously stolen Daiyousei's money and gotten her kicked out of the Youkai Market in A Very Nineball Christmas. And when he tries to get back at Cirno in chapter 15, Yuuka shows up and casually vaporizes him.
Elly (while fighting Youmu and Yuyuko): "Even in this world, where all rules are lightly enforced, there are certain predator-prey constants. Fire will burn, wolves will prey upon rabbits, scissors will beat paper, and against ghosts, Shinigami will always, always win. It's the circle of life and death."
Originally, Rin can adapt (slowly) to any magical projectile. Then, at the cost of her body, she gains the power of Mega Manning. By absorbing other people in a gruesome way.
When Yukari poisoned the ground to prevent Yuuka from growing plants in the battle field for her to exploit, Yuuka brought them in by useing herself as the carrier. Justified, due to being an Outer God, albet an extremly weakened one.
Eirin, of course. She wanted to do some experiments and studies on her pet's adopted daughter. It created the Blob Monster.
The Asakura Sisters, to a slight degree.
Mima is hinted to be the magical version of this.
Madness Mantra: Rin Satsuki degenerates into this, whenever someone usually Normal!Rumia even suggests that the Shadow Youkai may still be alive.
Madwoman in the Attic: Flandre. While the source material isn't definite as to how it applies to her, in Imperfect Metamorphosis she is this trope all over, introduced singing Sweets Time Midnight while using dead rats as marionettes.
Never My Fault: Despite being one of the main causes of the meaningless infighting throughout the story (by doing things like shutting down Eirin when she was trying to solve the situation peacefully), Yukari never even thinks she did something wrong. She even goes as far as to blame the riots in the Underground on Reimu, when she had been the one who had the brilliant idea of bringing Satori to the battle against Yuuka, and Reimu wasn't involved in any way in it.
Offing the Offspring: The Kirin society strictly, strictly controls who gets born when. As in, conception has to go through bureaucracy first. Literally. Rin? She wasn't just born out of misgauging; she was the result of a noble child's affair with a commoner, with the elopement occurring right when an Arranged Marriage was supposed to be finalized. And let's face it—to the Kirin, illegitimate children are a severe abomination. Despite what Reisen might have hoped, because of the layers of Things Meant to Never Happen, not only does Kirin society at large not want Rin back, they want her dead.
Oh Crap: Everyone who faces Ex-Rumia or Yuuka has at least one of these reactions. And on a few occasions hearing the latter's name is enough to provoke one.
And in chapter 41, when Rin gets serious, Yuuka suddenly realizes that she's no longer the biggest fish in the pond. And she's appropriately terrified
Offstage Villainy: Subverted with Mima. She has retired from her Evil Overlord business, so we just hear of her past misdeeds of which she is very much unrepenant and even proud. Then, in chapter 28, we see her nearly slaughtering the GPF agents because they arrested Marisa. And she would have, if Reimu and Marisa hadn't stopped her.
Out-of-Character Alert: A big part of how Reimu catches on to the fact that "Yukari" is actually an impostor in ch. 39; since when does Yukari speak in such a grandiose fashion?!
Oo C Is Serious Business: Chapter 44 shows that Elly has noticed the change in Yuuka's behavior since the events of The Storm. The poor reaper has worried herself almost to the point of insanity because she knows something is wrong with her master, but has no idea what she can do to help her.
Police Are Useless: Played With. Kotohime and the GPF are kinda serious and 'efficient', in spite of gathering some eccentric characters, but they have to deal with people like Marisa and Yuuka.
Porn Stash: Team Nine at first thinks this is what's inside the crystal box. Later, it turns out Marisa also thought this was how Patchouli would be hiding her porn. In ch. 34, it turns out Sanae has her own stash (whether portraying men, women, or both is not revealed)...or did, until Suwako noticed it.
"It is amazing, the sort of things people will do for love," Yukari murmured. She brought the teacup to her lips and slowly sipped the steaming liquid. "Even the proudest, the most uncontrollable, the most erratic of creatures can be swayed by its power. Mima is no different."
Kanako, on the other hand, is very much this. She complains a lot, but helps Reimu anyway, and she's not as cold and calculating as she wants to appear.
Satan a.k.a Lucifer: Implied to be the leader of the Angels that rebelled. Azrael was implied to be almost as bad as it was, but was too busy with killing everything it could to take control itself.
Science Is Wrong: If you ask Reimu, in any case. And, this being Gensokyo and all, she might be right. Blame Eirin.
Screw This, I'm Outta Here: Lily White, upon seeing how badly the reception to her announcing "IT'S SPRING" as well as the attacks by Ex-Rumia, decides to try again next year, hopefully by then everything will have calmed down.
Sociopathic Hero/Nominal Hero: Mima, not quite having gotten over her Evil Overlord tendencies but still firmly on the heroes' (or, at least, Marisa's) side. Would easily qualify for Token Evil Teammate, except that her side has some other very morally grey characters. Much to Reimu's dismay, Marisa takes after her in this aspect, if her encounter with Kotohime is any indication.
Shadow Archetype: Mima to Marisa. Apparently, Marisa takes after Mima a lot, so they are similar in many ways, such as their love of fight and explosions, their flirtatiousbehavior, and their calling everyone with nicknames. But where Marisa is straightforward, friendly, boisterous but well-meaning and certainly not a cold-blooded killer, Mima is sneaky, manipulative, ruthless and has absolutely no qualms about killing or horribly maiming anyone who gets in her way. Reimu's concerns about Marisa becoming like Mima certainly aren't unfounded.
The story itself, on the other hand, is still ambiguous: while, being a Dark Fic, it's almost required to have some cynical elements, the more cynical characters have been shown to be wrong, and the idealistic solutions aren't always the least practical. Of course, seeing how the fic is still ongoing, this could change at any point...
Spotlight-Stealing Squad: Yukari and Yuuka. Even if Yukari is one the main characters and Yuuka a chaotic element who only want to wreck havoc in the story, their interactions and confrontations have taken more and more screentime in the different chapters, culminating into The Storm. After that, Yukari's soul corruption and Yuuka's injuries will take them out of the story for quite some time, and the plot was refocused on Rin and Rumia.
Tarot Troubles: During Rumia's Journey to the Center of the Mind, she runs into Mima, who proceeds to read her past, present, and future, as well as that of several other characters (implied to be Rin, Yukari, Reimu and Reisen) through Tarot Cards.
Rumia is forced to stay within Rin Satsuki and sees every collaboration with her as this.
Reimu is gathering allies to achieve her objective, but these allies don't get along very well.
There's enough animosity between the Ringleaders (especially against Yukari and Mima) to ensure that nothing at all is likely to get done in anything less than an end-of-the-world scenario, and even then only with difficulty. Other than Yuyuko, Satori and her own Shikigami, almost all of the groups Yukari collaborates with have either one or both sides thinking ill of each other at best, or at worst actually betraying each other. And Satori's mostly cooperating for personally pragmatic reasons, to give her and her pets an exemption from being drafted for a task she thinks is worse.
And the crown jewel of the story's Teeth-Clenched Teamwork is the group Yukari drafts to kill Yuuka—one pair is genuinely on her side but is partly there to keep an eye on the least trustworthy combatant, one team is pragmatically cooperating, one team was blackmailed into it and their leader is pissed off at everyone who wasn't, one member was hunted down and offered it as an alternative to prison, then agreed willingly just because she wants to fight, and one member is royally pissed at Yukari and is only there because of another teammate. Fortunately the plan involves very little interaction between the teams and the way it goes Off the Rails involves even less.
"...and don't get me started on your reputation as godlike lovers. It seems that whenever you're brought up, people are either deathly afraid of you or they want you to throw them down and jump their bones. Sometimes both."
Villain Protagonist: Yukari Yakumo is a main character beside Rumia, Rin and Reimu. The "villain" part comes from her conviction that the safety of Gensokyo overrides everything else.
Walking Wasteland: Even touching Ex-Rumia is a risk of death, and is certain death to beings below a certain level of power.
Utsuho, after her Third Leg was broken. Only temporarily, though.
Well-Intentioned Extremist: Yukari, with emphasis on Extreme. Views on exactly how extreme or sympathetic she is varies among readers, but she is certainly capable of some very morally grey acts for (in her mind) the greater good of Gensokyo.
As an example, Yukari pulls a (fully crewed) oil tanker off Earth and blows it up as a weapon against Yuuka.
What Would Yukari Do?: Inverted with Reimu: when she asks herself if she really could commit evil or at least morally dubious acts to protect Gensokyo, she answers that she'd become exactly like Yukari.
Woobie, Destroyer of Worlds: Subverted with Rin Satsuki, since that almost everyone who at least know about her backstory believes her to be this, with Byakuren initially being the only exception. In chapter 12, Eirin even asked Reisen what she thought would happen if "she stumbled upon some human family out on a picnic", while it is shown later in the story that when Rin does stumble upon a helpless human, eating her by mistake, she promptly reforms her body and runs away apologising. Though it is understandable why everyone thought this after the battle of Eientei, as she was under the Shadow Youkai's control at that time.
Worthy Opponent: Yuuka sees Yukari as this and starts harassing her and interfering with her plans, partially out of this and partially because it's amusing to her.
Gambit Roulette: Yukari does this with basically everyone. The author even mentions it himself.
Xanatos Speed Chess: Mima states near the end of chapter 39 that any plan that she and the others might cook up is almost certain to fail initially, and that is why it is important that they start with a serviceable plan based on what they know at the moment, and when it fails, improvise.
You Monster!: Kazami Yuuka is treated as such - her very name frightens and disgusts people. Yukari states this reputation is well-deserved, since she used to destroy villages on a whim and it's very heavily implied she rapes and tortures people that wind up in the Garden of the Sun. And it may be because of something else about her...
Deus ex Machina: The way Kaguya, Mokou and Rumia are saved from the Zerg in chapter 4: a giant storm pops out of nowhere and slaughters most of the Zerg Subverted in that the storm was, in fact, summoned by EX-Rumia, who has... less than noble intentions for Mokou and Kaguya. And for the rest of Gensokyo, too.
Everyone Is Bi: Well, not everyone literally, but in the author's notes at the end of Chapter 6, TakerFoxx provides us with an insight about youkai sexual orientation in Gensokyo, and while Youkai who reproduce through conventional means like the Satori or the Kirin can have any sexual orientation, just like humans, and the same applies to Youkai derived from animals (they retain whatever orientation they had as animals), Youkai derived from concepts or inanimate objects are all bisexual.
Femme Fatalons: EX-Rumia uses these to horrific effect when separating a rabbit guard and his face.
Foot Focus: Noticeably, all three main characters go barefoot through the majority of the story.
Good Thing You Can Heal: The maiming and regenerating of our immortal protagonists simply does not end, and they're so entirely used to it that they don't even care (many minor injuries aren't even noticed until they physically impede whatever the victim was doing). The one with the least regenerative power suffers the least injury, however.
Remembered I Could Fly: In chapter 4, Ex-Rumia and Mokou are going down a steep path, and her companion has to remind Mokou that she doesn't have to descend on foot. Justified in that Mokou's flight had been disabled before, on two separate occasions (in chapters 1 and 2).
She does it again during the very next encounter, much to her embarassment.
Sand Worm: The dreadful velmick is a bioengineered sand worm. A lunar sand worm.
Karma Houdini: Averted. The tarantula youkai who steals Daiyousei's money and has her kicked out of the Youkai Market later harasses Cirno and gets frozen for it in Imperfect Metamorphosis chapter 4. And when he tries to get back at Cirno in Imperfect Metamorphosis chapter 15, Yuuka shows up and casually vaporizes him.