Ex-Rumia is like this too. She even calls herself the "Alpha and Omega" in Chapter 18.
Considering the Shadow Youkai is the avatar of Azrael, it could actually be coming from him instead. Since Azreal is a fallen angel, this would make a lot of sense.
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.
Anger Bornof Worry: Since many characters in the story are Jerkasses albeit heroic ones, this seems to happen a lot when their not teasing each other or genuinely malicious. Reimu becomes this after The Storm arc, and even Alice sort of counts, but another big one happens in the beginning of Chapter 38 with Patchouli to Remilia. This happens because of Flandre being killed (or captured) by Yuuka during The Storm arc. As tragic as it is, Patchouli notices she's a bit too over dramatic over it which does not fit her reputation, becoming a drama queen much like Rarity, or perhaps a Hikikomori not too different from Satou. Surprisingly, the scene afterwords is followed by a pretty big mix of Crowning Moment of Heartwarming AND Crowning Moment of Funny as Patchouli practically becomes a hero despite all of Remilia and Sakuya's snarking just before she's about to go to bed. The funny part comes from the fairies' reactions.
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.
Being Good Sucks: Well, more like being good is HARD, but Reimu finds it difficult to be a "people person" with how much harder the incidents in the story are to solve. Notably in Chapter 34 she realizes that rather than being anti-heroic, some the allies working together are more like villains working under an Enemy Mine and that being selfish and evil seems to make things a lot easier... Of course, because of things like her concern for Marisa following under the acquaintance of Mima, she'd still take the path of good.
Big Bad Duumvirate: So far, there's the Shadow Youkai and Yuuka. Honestly, it's kind of hard to know whose stronger despite the premise, but everyone believes it's still the Shadow Youkai. Then it turns out the both of them are WAY stronger than they appear, with the Shadow Youkai actually being an avatar of Azrael whose a fallen angel all just from it's sword and Yuuka is an Eldritch Abomination most likely straight out of a H.P. Lovecraft Cosmic Horror. Yukari thinks it's an Outer God while Mima thought it was a Great Old One. Confirmed by Chapter 41, The Shadow Youkai, whose only an AVATAR of a fallen angel is stronger than the Cosmic Horror Yuuka.
The Dragon: Regardless of that fact, Elly is still The Dragon to Yuuka. One has to wonder if she's terribly misguided and Obliviously Evil, especially since Yuuka acts oh so nice when she's not ripping someone to shreds.
The old Rin is like this too. Reisen can't even remember that she used to be like that when she reads her diary after The Storm arc, hoping it's just a phase. By Chapter 39, she rereads through it again and realizes that Rin doesn't discover it until 4 years later when Tewi stole it for unknown reasons, with Rin herself admitting she was a brat and being surprised. Reisen is obviously relieved.
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".
Cluster F-Bomb: The story itself, all the time, and the story is only rated T, among the other dark aspects such as implied rape. Takerfoxx himself was wondering about amping the story to an M-rating early on but by 51 Chapters, the story is still only rated T. It seems the ratings might actually be done by the site itself, not by the author's intentions. If not, then the rating is possibly Non-Indicative.
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.
For additional fun, Yuuka used to be an actual Lovecraftian Outer God. You know, the ones Cthulhu and his kin worship as gods. Since TakerFoxx is a troper, one has to wonder if he had this trope in mind when plotting that...
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.
Easily Forgiven: Cirno and Rumia are the only ones to forgive Rin Satsuki for what she has done.
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.
Yuuka's true name is Yidhra.
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.
And Elly actually IS British. Though she's not actually evil, it's just that she's loyal to Yuuka above everything else.
Evil Mentor: Mima to Marisa, causing several other characters to worry.
Evil Versus Evil: Yuuka vs. The Shadow Youkai. Well, if Yuuka can even be called truly evil if she has a bizarre set of standards.
Evil Versus Oblivion: It might also be this. Since the premise revolves around the Shadow Youkai, it might not be a spoiler for her to be said to be even stronger than Yuuka, but The Storm arc is 4 chapters long and Yuuka is still alive. The Shadow Youkai is just getting stronger too because of the inevitable power of Rin Satsuki copying legendary people's abilities.
Medicine Melancholy too actually, by Chapter 51. It's a long story, involving Marisa being close to killing someone because she was going to get arrested, but Marisa and Alice are pissed at each other with Alice refusing to talk to her for a long time. Marisa gets fed up and tries out all sorts of odd antics, one of them trying to give Alice's "friend" a black ball of soot. She actually EATS it. This is because she's a living doll, so she can eat anything, really. Could count as a Crowning Moment of Funny.
Alice: "Medicine, did you actually just eat that ball of soot?"
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.
Fanservice: Rinnosuke in Chapter 47. Takerfoxx even says he based it off of an Old Spice commercial.
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.
Freudian Trio: Played with: at first Reimu, Byakuren and Yukari seem a classical Freudian Trio with Reimu as The McCoy, Byakuren as The Kirk and Yukari as The Spock. As the story goes on, though (and thanks to Reimu's Character Development), we see that things are a bit different: Reimu, for example, in the beginning of the story is apathetic and easily annoyed, hates talking and mocks Byakuren's big speeches, while Yukari is cold, calculating and particularly fond of shooting the dog. As the story progresses, though, we see that Yukari is actually as irritable as, if not even more than, Reimu, and while she hides everything under a mask of aloofness, she's as emotionally involved as Reimu is, if not more. Reimu, on the other hand, learns to make impressive speeches and even convinces Yukari to go along with her plan by using logic. Byakuren, on the other hand, has stayed pretty balanced throughout the whole story so far, and has been one of the catalysts for Reimu's Character Development.
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.
Harsher in Hindsight: An in-universe example during Chapter 33. Rin had a dream that she wrote down in an old diary that she didn't exist but she was supposed to, and when she brought it up to people they didn't care and just ignored her. Reisen was reading through them and felt choked by it. Yeah... (Tear Jerker)
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?
I Have You Now, My Pretty: Yukari says this to Marisa in Chapter 20. Subverted though in that it's not what it sounds like. She's just trying to get Marisa arrested because Remilia was pressing charges. She even steals her witch and puts it on her head, saying the trope name.
"Uh-huh. Only problem is that it's wicked hard even when I've only got one person inside me-"
Chapter 47 is like this too, when Reimu thinks Marisa and Mima are having sex. Marisa is actually just exercising though. In a way it's Double Subverted because in the past, Reimu actually DID witness her having sex once quoted as being to "Reimu's disgust, Marisa's delight, and a poor farmer boy's absolute horror."
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 cruel Breaking Speech, she snaps in chapter 45. Luckily, Byakuren is always ready to help her get a grip on herself.
Remilia was feeling quite guilty after Yuuka took Flandre away and after her plan to take her back (by giving her Rin Satsuki, no less!) failed, but she is broken after Yukari's Breaking Speech and after realizing that while she was mourning Flandre, things got From Bad to Worse and she accidentally ruined Reimu's plans to solve everything pacifically. Hearing Reisen calling her and Sakuya out of it does not help.
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.
Jerkass Has a Point: Tenshi in Chapter 15. During a council meeting, Tenshi makes a point that while magical attacks may not work on the Shadow Youkai, physical attacks might, since Suika seemed to have done the most damage. Kanako even says "As much as I hate to admit it, she has a point."
Jerk With A Heartof Gold: Reimu and Marisa. During Chapter 32 called The Aftermath after The Storm arc, Reimu is actually starting to care about people more which surprises even her. Marisa on the other hand despite taking lessons from her Evil Mentor Mima has a lot of standards, such as caring for her friends like Alice. Heck, she even considers Yuyuko and Youmu as friends. Also, when Reimu visited Marisa and Mima when Marisa was sick, they actually laughed at how Reimu was worried about them, and Marisa felt bad to see Reimu having to leave so soon since there's a lot of people she had to visit (or felt like she had to, much to her annoyance.) It's actually pretty damn heartwarming.
Jerk with a Heart of Jerk: Mima. She may have her Pet the Dog moments with Marisa, but this is usually combined with giving her a stern lecture. On a more serious note, there's her rivalry with Yukari. When Yukari is beaten within an inch of her life against Yuuka from spiritual poisoning, she can barely form coherent sentences until Mima helps her. However, she didn't get rid of the pain which Yukari brought up. Her response was "Do I look like the altruistic type?" Yeah, she's kind of a bitch. Her final speech at the end before leaving was also rather rude. Even Yuyuko finds her to be still be rather unpleasant.
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 and Sakuya is forced with Remilia into exile at the Hakurei Temple when she gets called out by Reisen, Patchouli not only does not suffer any consequence whatsoever, she and Sakuya 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. She finally gets called for it by the Dream King.
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.
One-Sided Arm-Wrestling: Yuuka was just playing with Ran and, after some talking, lets Ran "win", breaking Ran's arm off in the process. In fact, Ran still obtains what she has came to, but still...
Original Character: The named Rabbit Guards, 'Tony' and Hunter. Subverted with Hunter. The disguise may be original, but that's actually Nue, whose supposed to be working for Byakuren but is going in the opposite direction.
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.
Police Brutality: Alice calls Yukari and Kotohime on this when they barge in her home in Chapter 20 when they try to arrest Marisa. Although she thought karma must be catching up to her and that she sort of deserved it, saying she was involved not even misdemeanors but "numerous felonies", she believed they were going too far in their actions. Furthermore, Yukari even tries to stop Kotohime from attacking the suspect after Marisa vaporized Nyoron, after that already happened because of Yuuka. She even thought of pressing further charges with "murder". Could count as a What the Hell, Hero? Moment. Of course, Mima is also pissed about the whole thing.
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."
This is also flat out implied in Chapter 49. Remilia honestly believes that Yuuka is going to rape her sister Flandre after capturing her in what could best be described as her Moral Event Horizon. Even Remilia didn't deserve that... In fact, her Break the Haughty moment has caused her to Took a Level in Kindness and give Reimu a huge Pet the Dog moment by offering the bounty money to her after capturing Rin Satsuki.
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.
Sarcasm-Blind: Rin Satsuki, all the time. It gets on Rumia's nerves a lot...
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.
The Blob Monster was this before being released by Team Nine. Almost an Inverted Trope, because Rin was more of a Sealed Woobie In A Can but was sealed for being dangerous.
The Shadow Youkai is a textbook example. As soon as the story is explained Yukari is forced to defend her decision to "only" seal it.
Secret Test of Character: Mima of all people gives this to Reisen in Chapter 37. Also, she wants the person to answer honestly by instinct, not from what she believes is the most logical and what the mentor in question wants to hear, although she'll ironically also state what she believes to be correct or incorrect. Go against the rules though and she'll get rather pissed...
Q. Who is the most evil being in Gensokyo? A. The Shadow Youkai Reisen first thought about Eirin, Yukari, Yuuka, and even Mima herself to fit the answer, but then she said it was the Shadow Youkai. Even Mima quickly agrees to this.
Q. Who is the most deadly (powerful) being in Gensokyo? Mima Reisen believes it might be Rin as much as she hates to admit it, but Mima believes it's actually herself, which scares the crap out of her, which leads to her wanting to use the same answer for the next question.
. Q. Who is the most dangerous being (most likely to cause harm) in Gensokyo? A. Reisen Reisen feels like saying Mima again to the point where Mima gets pissed and is about to strike her with lightning but ends up giving her a stern lecture instead about answering correctly. She then says it might be Reisen herself.
Self-Deprecation: Takerfoxx himself, maybe, especially notable by the end of Chapter 43 which is the Abridged chapter. This is in the form of writing a very long and complicated story that he himself isn't sure how to fix all the time.
Takerfoxx: I just made things more convoluted and confusing, didn't I? Goddamn it.
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.
Suspiciously Specific Denial: Yukari often tells Reimu that she's not trying to be a queen or anything of the sort... even when doing something that the head of a government would, like ordering death sentences, jailing people or diffusing interviews. Also, she's adamant about not letting oneself be involved emotionally... but is very emotionally involved in the whole affair, as both Reimu and Dream point out.
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: The Fool (Past), The Moon (Present), The Devil (Future)
Mima: "The Fool symbolizes the end of a journey, someone who is setting forth without fully knowing or understanding the hardships that await them. That's not a bad thing either, as it implies a certain amount of innocence... The Moon. It seems your days of carefree mischief are over. Now you are lost and unsure of your path. You are without a reliable guide, and do not know where your steps will lead... The Devil, the destroyer from within, will rise up and take control. Something... crippling. Perverse. Perhaps even evil. Usually it signifies some sort of flaw that you are allowing to hold you back through inaction. But here in Gensokyo the evil could end up being quite literal. I would watch my step if I were you."
Rin: Eight of Pentacles (Past), The Seven of Swords (Present), The Ten of Swords (Future)
Mima: "The Eight of Pentacles. The apprentice who desires to learn more. You have studied under a master but still wish to learn more. Ambitious, aren't you? The Seven of Swords. It would seem that despite all of the power you've accumulated, it isn't protecting you from the wiles of others. In fact, I'd go as far as to say that you are being betrayed, though not by someone you trust anyway. And now... Oh dear. The Ten of Swords? I'm sorry, but it looks like despite all that you do, it will be all for naught. Failure is your only option."
Yukari: The Empress (Past), The Hierophant (Inverted) (Present), Death (Future)
Mima: "The Empress. The creating spirit. And you've done quite a bit of that, haven't you? In addition, you are quite protective of what you've created. However, I would be careful of becoming overzealous... The inverted Hierophant. The false teacher. Except you aren't the one to take on a mentor, false or otherwise, are you? Well, I suppose this must mean you. Manipulative and deceptive. But is it for the greater good? A necessary evil? ... Unfortunately for you, your path leads to... Death. The end of an era. Depressing, isn't it?"
Reimu: The High Priestess (Inverted) (Past), The Seven of Cups (Inverted) (Present), The World (Future)
Mima: "The inverted High Priestess, the concealer of secrets. Are you keeping secrets to yourself, or has someone been keeping secrets from you? Or perhaps it is to be taken literally. After all, you're not exactly known for being vigilant about your job... What's this? The Seven of Cups? It's inverted as well! Looks like someone is getting a little fed up with deceptions and machinations! Good thing too, as this will lead to... The World. Ascension to something greater."
Reisen: The Fool (Inverted) (Past), Ten of Swords (Present), The Hanged Man (Future)
Mima: "The Fool inverted. You've had your naivete taken advantage of, haven't you? Innocent to begin with, but that hasn't exactly turned out well... Ah, you have a Ten of Swords as well. One wonders if things can possibly get any worse. I'd beware of asking that question, because it usually can. But all is not lost. For here we have The Hanged Man. Not as dismal as it appears. Look at the smile on his face. A sacrifice will be made, but it will be made gladly, and just might be beneficial toward you."
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.
The Needs of the Many: Yukari gives this speech to Reimu who then proceeds to turn the tables and show that Yukari's dictatorial attitude is what has prevented a peaceful solution and why her solution is the one most likely to cause gruesome collateral damage and losses.
"The Reason You Suck" Speech: Yuuka gives a very cruel one to Remilia at the end of chapter 42. Especially cruel because she mocks Remilia about Flandre's "death", rubbing salt in the wound.
Then Let Me Be Evil: Rin Satsuki to an extent in Chapter 40. She actually sucked in Mamizou on purpose partly because she wanted to, not just because she needed her shapeshifting powers.
"...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.
Wham Episode: Well, it's a Dark Fix so there may be numerous examples of this, but Chapter 45 is a pretty big one. It's all about what really happened when Rin Satsuki came to be the person that she is now. It's a pretty big case of Nightmare Fuel and Tearjerker. Yuuka was the one that relieved those memories for her, and she said it was more painful than actually turning into the Blob Monster that she currently is because all of those experiences were happening in a matter of seconds as she recalled all of those things.
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.
Who Dares?: Yuuka, all the time. It's one of the ways to see through her facade when she gets pissed off.
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.
That doesn't stop her from wanting to go "full bad-guy" if she has too. At the very least, it's pretty tempting. Despite Reimu trying to help her because of Byakuren and Reisen, even she doesn't believe she's that good of a person, yet she condescendingly yet sympathetically thinks of her as a kid. Technically, she's actually about 19.
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 Meddling Kids: Mima says this about the events of Mystic Square when it comes to ruling Makai in Chapter 37 saying she was only stopped because of Reimu. "That meddling shrine maiden".
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.
Expendable Clone: Rumia's opinion about Kaguya once she starts losing her temper. Also, Mokou's plan for the finale.
Femme Fatalons: EX-Rumia uses these to horrific effect when separating a rabbit guard and his face.
Foregone Conclusion: Downplayed: we know that neither Kaguya and Mokou nor Rumia Yagami have managed to get out of Rin's body because the Time Skip in the main story does not affect Rhapsody of Subconscious Desire, which means that by the time the Time Skip has happened, RoSD has already ended. We still don't know what has actually happened, though.
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.
Ironic Echo: Rumia warns one of Kaguya's figments not to try stabbing her in the back with some pithy one liner like "Here's your exit!" Later, it literally stabs her in the back while shouting the same line.
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.
World of Snark: Given that the only real characters here are Gensokyo's three biggest DeadpanSnarkers, and the whole sidestory takes place inside their minds, it's bound to happen. Every time someone opens their mouth, one time out of three it will be to snark about one of their travelling companions.
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.
Tropes contained only in The Sorceress's Apprentice:
Awesome, but Impractical: The Receptacle for evil magic users. Not only does it take 50 years to "charge up", its requirements for a sacrifice are very precise (see Powered by a Forsaken Child), all for destroying any physical object in an untraceable way.
Child Prodigy: Mary (aka Marisa), who has no magical ability whatsoever but instantly grasps runes better than what most adults ever manage.