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Action Mom: When Shinki is introduced in Shenanigans in a Magical Forest, the Boss Subtitles go through several titles relating to maternity and divinity before settling on "Almighty, Like All Mothers".
Alternate Character Interpretationinvoked: Mokou was actually a lesbian who was jealous of Kaguya's suitors, but never realized this until Remilia manipulated their fate so that they'd fall in love; Kisume is completely freaking nuts, and reasons that only someone who is insane would want to live in a bucket the way members of her species do, and it is implied that all tsurube-otoshis are like this.
Anachronic Order: a side-effect of throwing in "this takes place between Subterranean Animism and Undefined Fantastic Object" after the fact. In particular, Rethinking the Natural Law initially cheerfully and strictly followed the reverse order of the available story modes in Touhou 12.3; this was also the optimal order to avoid actually revealing anything, including the identity of the new villain, until the arc was more than halfway over. The timeline was once the subject of frequent retcons.
Angst? What Angst?invoked: Orange is stated to be a "youkai of resilience who recovers more easily than [she] fears" by Hina; she's less bothered by the fact that she was sealed away by Reimu for eleven years (according to the timeline) than she is by everyone smothering her in worry and concern.
Artists Are Not Architects: The continual difficulty scaling the characters in relation to one another (i.e. Flandre changes sizes during the Catness ark so that she can be smaller than Remilia, but larger than Cirno). However, Muffin since created a scale for character-sizes which was applied to every comic since #92 or so.
Also pointedly averted with respect to Rin Satsuki's Mysterious Past — the characters obviously know what happened between Rin and Yukari, and they keep referring to it, but no explanation has been forthcoming so far.
Bad Powers, Bad People: averted; apart from canon ones like Yamame, Flandre, once her "destroy things" power gets upgraded to "Manipulation Of Destruction," uses it to heal people (by "removing" the destruction). And Medicine, once she gets over her hatred of humans, is actually really rather nice, if a bit shy.
Big Bad Wannabe: Meimu, jealous of Reimu, Yukari, and Marisa's fame, travels back in time to try to steal Reimu's thunder by interfering with "the Hisou Tensoku incident," and then, implied in a future-timeline comic, use her prior knowledge of Incidents to solve them ahead of Reimu and Marisa.
She was tall, limber, and positively reeked of strength. Not power: strength. She wasn't very imposing as far as musculature went, nor did she radiate magical force, but she seemed to have nerves of steel, an iron will, a grip that could crush titanium, and a chest which, um, actually, let's stop that metaphor right there.
Butt Monkey: Averted — Muffin has professed a deep "haet" for the fan community's habit of abusing certain characters (particularly Alice and Meiling) and, in some cases, has set up happy and stable relationships for those characters. At one point this went as far as creating comics specifically to show victories for certain characters who had been shown to lose in previous incidents, though whether that actually works is up for debate.
Canon Discontinuityinvoked: Ellen has been stricken from Nekokayou's version of the Touhou canon, being that she was originally from a non-ZUN work (of course, being a PC98 character, her position in Touhou canon is shaky anyways).
Cerebus Syndrome: averted; there are one or two multi-part arcs, but it always goes back to the original one-shot setup, and it retains the humorous tone. The more serious stories are reserved for the surrounding fanfics. Also parodied with the out-of-continuity "It's REALLY epic!" comics.
Crack Pairing: Apart from Mokou x Kaguya (they want to kill each other in canon), Kimiko has shipped Cirno (fairy with ice powers) with Utsuho (hell raven with the power of a three-legged crow with the power of control over nuclear fusion), solely over the "cold fusion" pun (and the fact that Cirno is known as a ⑨, while Utsuho is a ⑥). Muffin has also made a few peoples' heads explode by merely suggesting Shinki x Daiyousei (that is, a world-creating Final Boss goddess and a Mid Boss fairy, respectively). Invoked with the random pairing generator on the site.
Crapsack World: According to Word Of Muffin, the Outside World must be like this (for magic-users and youkai if not necessarily for the Muggles), given the implications of the fact that Gensokyo is (a) a world of illusion, where things exist if enough people actively disbelieve in them in the Outside World, and (b) a paradise where nothing seriously bad happens in the long run.
Deconstruction: Touhou's canon is extremely vague on a lot of things. Muffin sometimes takes a particular aspect of canon and says "Okay, so ... how would this really work?" about it (see above, under Crapsack World).
In particular, Meimu/Kon Yakumo's depiction was meant to deconstruct the Mary Sue archetype: on top of the idea of "Meimu" to begin with, she is the daughter of a canon character and she barges into the plot of one of the games to try to make herself all important, but she is a bratty idiot and everyone realizes this (on top of having a power which resembles Yukari's, but is much less versatile or useful). The execution, however, was a bit lacking.
Gratuitous Japanese: The title, which translates to "Oriental Cat Prettyface"; Muffin freely admits that this was "because I am a dork." (Incidentally, none of the Japanese Touhou-fans who are aware of it seem to refer to it by that name.)
Homosexual Reproduction: Carroll, who refers to Alice as her mother and Marisa as her "father." Shanghai, who was merely created, refers to Marisa as "other-Mom." Mika and Midori also had fun once considering this idea with respect to Kaguya, in light of the existence of Kaguya the mouse.
Infinite Canvas: The comics are variable-length after the third one or so, ranging between Yonkoma and the 35-panel monstrosity comprising the climax of the Catness arc (which also had a long panel at one point); this has gotten to the point where Muffin has begun breaking the comics into two files by default to keep their hugeness from bogging down peoples' connections. Furthermore, several comics randomlychangethings every time the page is loaded...
Interspecies Romance: See most of the entries under the "shipping" link. Human/human-turned-magician (though Marisa changes down the line, too), ghost/half-ghost, vampire/satori, ice-fairy/hell-raven ...
Meimu: Maybe you're the strongest fairy there is. Maybe. But you're still weaker than even a human, and all your opponents will still very easily outwit and curbstomp you, especially with that stupid "Icicle Fall" Spell Card.
Cirno: Hey, I haven't actually used Icicle Fall in like months.
It's All About Me: Meimu. The best example of this is when Rin Satsuki reveals that she was a Fake Defector, citing the fact that Meimu was trying to get her to go against her best friend. Meimu replies, "You don't care about me at all, do you!?"
Noodle Implements: One of the ways Kaguya once killed Mokou. The "kinky" variety also somewhat occurred in-character in an inverted fashion in comic #16 when Aya overheard Marisa saying "I bet you didn't know I could do that with a mini-hakkero!" (she was tickling Alice's hitbox with it) and immediately assumed that something more naughty was happening.
One Steve Limit: Touhou itself, with its Loads and Loads of Characters, has been an example of this trope for years (Rin Satsuki and Rin "Orin" Kaenbyou notwithstanding), but Muffin has expressed a desire to maintain the trope within the webcomic: having declared the original Ellen not part of the Nekokayou canon, he promptly appropriated the name for the otherwise nameless-in-canon Tokiko, since there's no way that he can accidentally duplicate a ZUN-created name that way (apart from Rin Satsuki and Satsuki Hakurei).
OC Stand In: Marisa's father Daisuke, who doesn't have so much as a name in canon, and Rin Satsuki, who had a name in canon and not much else.
Two particularly unusual examples are Meimu (AKA Kon Yakumo), who was already a sort of public-domain OC, but Muffin created an entirely new backstory for her which was only partially based on the "original" version; and Shanghai Margatroid, who was simply a magically-controlled puppet in canon until Alice and Marisa made her into an Independent Doll in the ending to Shenanigans in a Magical Forest. Then there's EX-Rumia, AKA Rumia Yagami ...
The Yatagarasu got introduced as Yasora Kojiwa in Shenanigans in a Magical Forest ... and was then killed one strip later. (Her ghost remains, however.)
Character sheets for all of the above can now be found here.
Painting the Medium: In the fan fiction, spoken dialogue in English is given in an italicized serif font (except in cases where it's really obviously not in Japanese-plus-Translation Convention), and Sakuya's Time Stop gets its own coloring as well. In Create.swf Adventures, dialogue and the names of certain items (including most characters) are colored blue when they're supposedly literally in English, green for Romaji, and red for "Japanese-plus-Translation Convention."
In the first act, the players aren't controlling the characters in the "Player Character" sense of the word; rather, the "commands" the characters are receiving are from bizzare spirits, a side effect of an overabundance of magical fungal spores. The characters who discover this start working against it. That's right: the characters were fighting against the players.
In the second act, the main character is Masha Kinoko, a youkai "born" from the mushroom that produced the aforementioned spores; the Player Characters are no longer the result of "WEIRD POSTMODERN SHIT." Also, Marisa visits Muffin's site at one point, and finds a Create.swf Adventures page made in 2016 — which is to say, six years after the comic was created.
In the third act, the main character is Utsuho Reiuji, but the players aren't directly controlling her. Rather, the commands are going through the yatagarasu she consumed — and said yatagarasu is mostly failing fantastically at Grand Theft Me, mostly due to Utsuho's Cloudcuckoolander, Too Dumb to Fool tendencies.
"Act ⑥" (the fourth act): It is revealed that this is all an "ADVENTURE-GAME / RPG / DANMAKU hybrid" being played by Muffin, and that KirbyM (who is a different individual from "Walfas") is the creator of it and Touhou Nekokayou as a series of adventure games, which were made with the aid of Create.swf. On the page in which Muffin becomes the "Player Character" ("Thou art I, and I am thou You are now MUFFIN."), it alternates between first-person and second-person narration. Soon after, Muffin starts cheating at the game, giving the characters God Mode, and wrestling with the game's anti-cheat measures.
Plot-Relevant Age-Up: Alice, who became a youkai and stopped aging when she was fifteen, is using a spell so that she grows up along with Marisa (who was, of course, still aging nine years later). Remilia and Flandre have since gotten Patchouli to create a similar spell that works on vampires, though they both usually stay in their younger forms.
Sakuya: "Well, I meant that my lady and I take exception to trying to kidnap Meiling like that. It was therefore a fatal error."
Rainbow Speak: In Create.swf Adventures, text is colored red for text "translated" from Japanese, blue for text "already in English", and green for romaji. Outside of dialogue, in which everything is one of these colors, the coloring tends to be reserved for key-items (and capitalized, in Shenanigans in a Magical Forest).
Retcon: Dissatisfied with how comics 97-100 turned out, Muffin tossed them into a bin and basically started remaking them. To say nothing of the timeline ...
Retired Badass: Sakuya, not that it stops her from being badass nowadays.
Rule of Funny: The Catnessarc, in which half of Gensokyo's not-already-Petting Zoo People population gets turned into cats, and in which "shiny objects" is a technical magical term, and susceptibility to the effects of the catness is based on stupidity or strength (but not both). And that's just the tip of the iceberg in the comic as a whole ...
As of April 1st, 2010, Muffin's updated the comic's main page to this:
...updated whenever I feel like it (generally ends up being around Monday-ish, though the original intended time was Sundays and occasional Wednesdays or Thursdays, but ultimately "when I feel like it").
That's nothing compared to the prose fiction. Of the five multi-chapter fics, only one is finished and only two of the other four have been updated since 2010.
As of October 2, 2010, the comic was officially on indefinite hiatus, although Muffin was still doing Create.swf Adventures. It came back on the 10th of April, just a few days after the end of Shenanigans in a Magical Forest.
The comic was put on another indefinite hiatus on December 17, 2011. Cottagesnagged is still ongoing, but Muffin has implied that he might stop doing much in the way of fanworks when it ended.
Schizo Tech: They've been in Medieval Stasis since 1884, but the Moriya Shrine and Yukari have started bringing in electricity and computers (Yukari even brought in television and computers before Subterranean Animism), leading to this.
In addition to Metal Gear Solidparody episodes, the "Time Paradox" gag from MGS3 is often used, not to mention that Nitori has developed a knockoff CODEC technology which has seen use outside the direct parodies.
At one point in Cottagesnagged, we see a CODEC device's box, which has a picture of a metal gear.
Sakuya is a walking Shout-Out to Dio Brando. This is in Touhou canon. The trope is present here by way of the fact that when she uses her Time Stop ability, the declared spell card is always (the technically canon) "ZA WARUDO" and the fact that Muffin is responsible for KirbyM including Dio-Sakuya poses in create.swf.
Marisa's "NO WAY! THAT'S IMPOSSIBLE!" line is borrowed from KirbyM's ouvre, as is the punchline for #84 ... though the line in KirbyM's flash is said for entirely different reasons.
The entirety of "Create.swf Adventures" is a shout out to MS Paint Adventures, using many of the running jokes established therein (the pumpkin, the retrieval of arms, the Added Alliterative Appeal of the Strife Modus screen...), with Rumia's "Team ❽" forming a parody of the Midnight Crew.
Kisume can apparently travel between buckets by "following recipriversexclusions of [her] mind and soul." Sakuya then describes the term when asked (though obviously not referring to the book by name.)
In comc #37, a bit of text in the second to last panel is qrrbrbirlbel. Oddly enough, this one was NOT picked up quickly.
Sliding Scale of Idealism Versus Cynicism: It falls firmly towards the "idealistic" end, but with a certain amount of cynicism. For instance, Eiki Shiki's KotOR-Karma Meter places Reimu on the good end but closer to the middle, with a note to the effect that this is "slightly below normal people" (although presumably Eiki Shiki's Karma Meter is all about the more stringent requirements of getting into Heaven).
Speak of the Devil: Muffin keeps track of hits to his site and where they're coming from. This enables him to pop up on message boards where people have linked to his site ...
Watsonian Versus Doylist: Occasionally, Muffin explains discrepancies and plotholes ("How did Koishi immediately steal Red The Nightless Castle from Remilia? According to Grimoire of Marisa, Satori needs to use Terrifying Hypnotism first!") with both forms ("I haven't read all of Grimore of Marisa/she got it from Flandre earlier").
Webcomic Of The Game: There was a Story Arc which parodied Embodiment of Scarlet Devil, as well as comic adaptations of each of the 12.X storylines.
What Kind of Lame Power Is Heart, Anyway?: Among the original characters, Mika has the ability to manipulate wind in leaves, and Midori can manipulate flavors. Although Tewi was clever enough to come up with a simple prank using them ...
The Worf Effect: Parodied in the out-of-continuity "it's really epic!" comics, which are a reaction to several fanfics Muffin read which, in order to take on an "epic scale," killed off major characters just to show they mean business!
Yandere: subverted when Yukari and Tewi tried to pull a prank that involved manipulating the Border of Tsundere and Yandere, only to discover that Alice wasn't an actual tsundere anymore - she was all out of "tsun".
You Gotta Have Blue Hair: Pretty much all canon; explained for the human characters by way of Gensokyo's naturally-high magical energies (i.e. Sanae had black hair in the Outside World, but entering Gensokyo turned her hair green), and for the youkai characters by the fact that, well, they aren't human, so obviously the rules are different. Muffin also created a version of KirbyM's Daily Flash characters with more realistic Japanese hair colors after previously depicting them and Sanae straight-up in an Original Flavor comic as a birthday present for KirbyM.