Mikiya Kokutou becomes intrigued by the mysterious series of violent deaths occurring in his town and Shiki Ryougi, a beautiful but unsociable girl. As he tries to become closer to Shiki, he realizes that Shiki is connected to the mysterious deaths and that the supernatural forces involved with both could kill him. It is revealed that in Shiki's family, certain members of her family possess two distinct personalities, both aware and conscious of one another, but possessing different qualities. The dual consciousness, and Shiki's upbringing as a demon hunter, has caused her to reject other human beings.
However, upon meeting Mikiya, she gradually finds happiness through their relationship and a schism develops between her two personalities. As a result, she winds up in a traffic accident and is left in a coma for two years. When she awakens, she finds herself unable to connect her past memories to her current identity. Reunited with Mikiya, now employed as an investigator for Touko Aozaki, Shiki assists Touko's detective agency, Garan no Dou, whenever combat is required, while struggling to come to terms with her identity.