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Adaptation Distillation: Probably in an attempt to make it less confusing and more generally appealing, the anime removed (in its first season) all the things going on in the real world. This effectively deals with the massive Mind Screw that shows up later in the manga.
All Just a Dream: It's implied that the events in Amatsuki could just be Toki and Kon experiencing lucid dreams at the hands of a crazy scientist and some mysterious mind-control device.
Alternate Self: The characters in Amatsuki are either based on people from the present day, or actually are those people trapped in virtual reality. Most have no knowledge of the real world, and bear only subtle resemblances to their other selves, in one case even switching genders.
Anti-Hero: Pretty much anyone can qualify for this, but mostly Bonten.
Art Evolution: The characters have steadily become softer and more fluid. Early artwork is almost unrecognisable compared to what was drawn recently.
Author Appeal: Takayama Shinobu really loves drawing her characters in fashionable modern Japanese street clothes on cover pages, with plenty of hair accessories (especially on boys). Most artwork also seems to depict the characters stuffing their faces with food. Toki has worn fox-masks on a number of occasions. And then there's Kon and his Oral Fixation...
Break the Cutie: Tsuruume after the reset. This trope also applies to Toki himself after he loses Kuchiha and Kon as a consequence of his own decisions, and if we get to count the past, Hiwa/Bonten, Shinshu, and Ginshu. Though one might argue that Ginshu was broken from the start.
Kon, who turns up right at the beginning and later appears in Amatsuki as a major character. Also Ainezu, briefly introduced as a nameless doctor and then forgotten, only to turn up much later as a member of the infamous Divination Bureau.
Imayou and her master the tree spirit, who was reborn, show up to help rescue Tsuyukusa from the centipede demon poisoning the forest.
Kosen, a young monk from Sakagami Shrine introduced in a side story, is revealed to have been turned into Kon's Clone by Conversion after the reset.
Hair Colors: The series mostly has realistic hair colors. All Japanese have black hair, unless (and we're looking at you, Toki and Kon) they've colored it. Even some demons have realistic hair... until Tsuyukusa decided to break the mold by going green.
However considering he's a tree, I think we can let him off on that one.
Humans Are the Real Monsters: While they may not be evil, none of the humans introduced so far are above manipulating everyone around them for their own benefit. But the demons have their bad points too, most of which are born of revenge against human actions.
Ironic Nursery Rhyme: "Toryanse", a traditional Japanese children's song which is used to incredibly creepy effect, especially when the Yakou is involved.
Jigsaw Puzzle Plot: Just continues to get more and more confusing as time goes by. Even over 100 chapters in, we still know very little about the main characters or the connection between Amatsuki and the real world. While there have been various hints, these are few and far between, and hard to fit together.
Used symbolically at the end of Chapter 99, when the pieces "snap into place" for Toki.
Josei: Although it gets mistaken rather often for Shōnen.
Kid-anova: Despite appearances, Toki has proved to be awfully good when it comes to the lady types.
Bonten: "He's got a way with women..."
Tsuyukusa: "He'll talk his way right into bed at this rate..."
Knowledge Broker: Hashita, Shiraai, Aonibi, and Wakasa are all part of a spy organisation dealing in stolen IT.
Bonten believes that absolutely everything Toki says is the truth, because, well, he's the Blank Page.
Let's Get Dangerous: Sure, Toki noticed sword calluses on Beni's hands, but it's a different matter when she's suddenly moving at super speed...
Loads and Loads of Characters: It doesn't help that readers are constantly trying to match the characters from the virtual world with their real world counterparts. It's not as easy as one might think.
Lotus-Eater Machine: A clam demon traps Kanzo in an alternate childhood born of his secret desire to be free of the Inugami. Toki and the others are also pulled in and have to find a way to wake him up.
Kill It with Fire: Kanzo, ostensibly to rid himself of any more weakness, sets the whole illusion ablaze and boils the clam demon alive.
"Amatsuki" is an abbreviation of the term "Amayo no Tsuki", which means "moon on a rainy night", i.e. something that cannot really exist. Bonten believes that the world of Amatsuki is an illusion.
Midori Sensai's name is brought attention to in-story. Shiraai links the "thousand-year-old green" colour to a hypnotic, dreamlike state.
Merged Reality: The demons aim to achieve this... by devouring all humans and destroying Amatsuki altogether.
Miko: There are many traditional examples at the Sakagami Shrine.
Mind Screw: The anime is for the most part fairly straightforward. The manga, on the other hand, quickly proves everything the characters originally believed to be false, and then rather than solve any mysteries it just keeps opening up more and more. Things started to become set in stone approaching Chapter 100.
Monochromatic Eyes: Whenever Sasaki actually does open his eyes, they are completely white. This also applies to Kurotobi and Benitobi, whose eyes are almost completely black.
Mood Whiplash: The series likes to yoyo back and forth between heart-rending tragedy, ridiculous comedy, bursts of action, lengthy plot explanations, and friendship.
Mr. Exposition: Kon mostly. Ginshu, Bonten, Kurotobi, Tsuruume, and Hashita tend to dabble as well when required. In fact, this trope applies to pretty much everyone except Toki.
Mysterious Past: All the main characters, though Kuchiha, Ginshu and Bonten have had theirs explained somewhat. Toki's is still fragmented and downright confusing, whilst Kon has virtually no backstory whatsoever.
Nice Job Breaking It, Hero: Happens again and again and again, since Toki has the powers of a god and no idea how best to use them.
Ninja: Sasaki commands a whole group of them, two specific examples being Kurotobi and Benitobi.
Obfuscating Stupidity: Ginshu is fairly effective with this in his/her entrance, but really peaks in the flashback "The Butterfly's Dream" when he/she first interacts with Bonten.
From the start Bonten doesn't hide his knowledge of the modern world, however it's not until much later that he reveals he also knows the true identity of Teiten.
Turns out Kon is the absolute master of this.
Oh, Crap: After Toki stabs a mirror demon... and then it shatters and he realises he's about to get pelted by hundreds of shards of falling glass.
Only One Name: Multiple, including anyone not human and generally the people associated with the supernatural.
Invoked when Heihachi asks Kon why a regular guy like him has a family name, since only samurai and nobility had them in the Edo period.
Orphean Rescue: The heroes must travel into an illusion of the hellish Spirit World (which is also a gateway to the past) to try and rescue Kuchiha and the Shogun.
Parental Abandonment: Toki's parents didn't want him. Kuchiha is an orphan, as was Ginshu, and Tsuyukusa lost his only parental figure when he was young.
Parental Substitute: Suoh and Chitose, who took care of Toki after he was sent away from home. Hashita also rescued Lily from her abusive father and officially adopted her.
Posthumous Character: Suoh, who died under mysterious circumstances sometime before the start of the story. There's also Byakuroku, although technically his soul lived on in Ginshu... until Ginshu dies, that is.
Powers That Be: The god Teiten, and to a certain extent the other members of Heaven's Seat.
Pronoun Trouble: It's tough talking about the genderless Ginshu in English.
Screw Destiny: The entire plot is driven by people trying to use Toki's power in order to change the fate that has been assigned to them.
Sexy Backless Outfit: Bonten regularly wears one, accentuated by the fact that he never puts his haori on properly. Kon joins in on the second volume cover (see above picture).
Shotacon: Both Sasaki and Kurotobi seem to have a thing for young Toki, Kurotobi being in the habit of calling Toki cute and at one point apologizing for staring. Sasaki, on the other hand, just seems to enjoy being creepy.
Sliding Scale of Silliness Versus Seriousness: Amazingly so far the manga has managed to stay firmly in the middle, never having too much of one without the other to balance it out. The anime however was planted firmly on the Serious side of things.
Spirit World: The demon paths connect the human world and the spirit world, allowing demons to travel huge distances in a matter of minutes. However, their world is implied to be a sinister place, the paths are deceptive and losing your way means being trapped forever in purgatory.
Spotlight-Stealing Squad: Bonten's group have appeared on almost every cover since Volume 7, meaning, aside from Toki, few other characters take centre stage.
Sprouting Ears: Particularly Kuchiha (which makes sense, since she's a dog god) and Susutake when he's being mischievous.
Super-Deformed: Happens all the time in the manga, when characters tend to go chibi for absolutely no reason, other than comic relief.
Teen Genius: Midori Sensai graduated university when he was about 14. Also, according to later chapters, Kon is a highly tech savvy hacker.
Colorful Theme Naming: Very nearly all the characters are named after traditional Japanese colours used in painting and fabric dyes.
Floral Theme Naming: As can be expected, several characters are named after flowers, like Ayame (iris), Kanzo (daylily) and Tsuyukusa (spiderwort). The chapters are also frequently given floral titles related to hanakotoba.
Animal Theme Naming: Many names also have a double meaning as birds, such as Toki (ibis), Kurotobi (black kite) and Suzume (sparrow).
Chapter 81 - It's confirmed that everyone in Amatsuki is an "avatar" of a real world "player".
Chapter 95 - There are two Kons. The Kon who lost his memories was actually a doppelgänger created by the real Kon, who's aware of Amatsuki's true nature and has powers similar to Bonten. The ending of Amatsuki's "plot" is also wholly dependent on Toki's decisions.
What You Are in the Dark: The mirror demon in the castle uses its ability to reveal demons' true forms and people's true nature to intimidate Bonten, Kon and Toki.
Wild Card: A lot of the characters work for this, but possibly Toki as the best example, since he will always choose to help people no matter the consequences.
Wouldn't Hit a Girl: Subverted because although Kon has no qualms assisting in the smackdown of Tsuruume, he doesn't actually hit her at any point, and Toki scolds him for fighting with girls.
Year Inside, Hour Outside: When Toki is transported to Amatsuki, Kon has apparently been there two years already, despite Toki having seen him in the present time just minutes beforehand.
90% of Your Brain : The "ten percent" myth is used in Chapter 48 by Urushibara, a crazy doctor trying to push the limits of the human body. It remains to be seen if Lily develops any special abilities related to this, or if the other unusable 90% has any part to play in the two-worlds plot.