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Ichiro Inuyashiki is down on his luck. While only 58 years old, his geriatric looks often have him written off as a pathetic old man by the world around him and he's constantly ignored and disrespected by his family despite all that he's done to support them. On top of everything else, his doctor has revealed that he has cancer and it appears that he has little time left in this world. But just when it seems things couldn't get any worse, a blinding light in the night sky strikes the earth where Ichiro stands. He later wakes up to find himself unscathed, but he soon starts to notice that there's something…different about himself.

Ever since the School Island Incident, in which the four Kings were involved, the Silver Clansman, Kuroh Yatogami and Neko were on their search for their master Shiro. Unable to find any leads to Shiro, the two were in a gloomy mood until they ran into Homura members, Rikio Kamamoto and Anna Kushima, who were apparently being chased by someone...

The story revolves around high school student Akira Nikaido, a typical slacker living a normal life. That is, until he meets the mysterious Shirogane, a man who suddenly appears and tells him that they have a destiny together. When Akira hears this, he is shocked and doesn't believe a word of it. Aya, a friend of Akira, forgets something in the school one night, and asks Akira to help her and go find it. He agrees, and while there, he gets attacked by a shadow monster. Shirogane convinces him that the balance between the human world and the shadow world has been distorted and that Akira must become a "shin"- a creature of the shadow world- in order to help restore the balance. The anime has shonen-ai themes which are completely absent from the manga.

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...