The story is set in Nagasaki prefecture in Minami Shimabara city, the fabled origin of the Shimabara Rebellion that sent shockwaves through all of Japan in the early Edo period. It is also where a third-year junior high school student named Shirou spends his days with his school friends. One summer day, Shirou's older childhood friend Akane returns to Minami Shimabara from Tokyo. Shirou and Akane take a stroll around Minami Shimabara with another longtime friend, Tokiya. While these friends are dealing with nostalgia and more complex feelings, a mysterious creature named Goron suddenly appears before them. This encounter with a mere little creature causes great events to unfold once more in this city... (Source: ANN)

During a blizzard, Masayuki Muroi's old high school friend pushes him off a mountain to certain death. However, Masayuki survives the fall and escapes to safety thanks to Yuki-Onna, the spirit of a beautiful young woman who is said to lead men to their demise—but all she asks in return is money. Eleven years later, Masayuki has lived a successful life, having gotten married and amassing a great fortune. But when his company collapses and his wife cheats on him, Masayuki retreats to the city where Yuki-Onna once saved him, and he reconnects with her by offering her money and tasty meals. While Masayuki recovers from his misfortunes, another one knocks on his door: his ex-wife is found beaten to death, and now only Yuki-Onna—who cannot reveal herself—can corroborate his alibi. With no one to turn to, Yuki-Onna enlists the help of the spirits' God of Wisdom, Kotoko Iwanaga. Revered by the various spirits that wander the earth, Kotoko uses her extraordinary wits and cunning to solve all quarrels they may have. In her duty to protect spirits and humans from colliding, Kotoko drags along her immortal boyfriend, Kurou Sakuragawa, and promises to prove Masayuki's innocence without exposing Yuki-Onna's existence.

The Layton Detective Agency, a business that helps its clients solve unusual mysteries, is run by Katrielle Layton—daughter of the world-renowned archaeology professor Hershel Layton. Together with her assistant Noah Montoir and talking dog Sherl, Katrielle finds herself unraveling cases involving a newly purchased cursed house, a dress imbued with a demon's curse, and the zombie of a client's deceased spouse, just to name a few. Aside from her more quirky cases, Katrielle has been working on another unsolved problem: the disappearance of her father. Founding the agency was only the first step in her attempt to uncover the truth behind his vanishing. As she continues to take on client after client, each with wackier and stranger issues to tackle, Katrielle steadily closes in on the answer to the biggest mystery of her life.

In 18th century Paris, a coffin is found floating down the Seine River. It carries the corpse of noblewoman Lia de Beaumont: a spy of King Louis XV, and whose younger brother Charles d'Eon has just been knighted. When several disappearances occur throughout Paris, the young knight believes that they are somehow connected to his sister's death. Hoping to find her killers, d'Eon joins the secret police to investigate the incidents. Following the clues, they piece together that a conspiracy between members of the French and Russian nobility, spurred on by a cult, may be behind the disappearances. D'Eon concludes that Lia may have uncovered the truth while on a mission and was killed as a result. That night, the secret police are to arrest the Duke of Orléans on suspicion of being the mastermind. One of their own transforms into a demon called a Gargoyle and massacres the group. D'Eon attempts to rescue the sole survivor, only to find that he too has been transformed. During the ensuing battle, d'Eon is possessed by Lia's vengeful soul, who takes command of his body and slays the Gargoyle herself. In the aftermath, d'Eon must gather allies to discover the depth of this supernatural conspiracy.