A teenage girl possesses the "Mystic Eyes of Death Perception," a supernatural power that lets her see the "death" inherent in all things and destroy an object by severing its "origin." She has just awakened from a two-year coma caused by a car accident. Before the accident, she had two personalities: a male one called Shiki (織) and the original female personality, also named Shiki (式). Children born into the Ryougi family are normally male and are raised with two personalities, so the male personality is traditionally termed the "yang" personality and the female the "yin" personality. Which Shiki is speaking at any moment can be determined by their distinct speech patterns—most notably, the female Shiki uses the pronoun watashi (私), while the male Shiki uses ore (俺). After emerging from her coma, Shiki finds she can no longer sense the male Shiki's presence and believes he died in the accident. She also feels disconnected from her pre-accident memories; although she knows she is Shiki, she does not feel like she is. In an attempt to recover herself and the "dead" Shiki, she adopts a cold exterior that resembles the male Shiki's demeanor and tries to behave as the female Shiki once did. Touko understands the sense of detachment Shiki experiences but considers the current Shiki to be a third, entirely new personality.
The series is set in the same universe as another TYPE-MOON work, Tsukihime. Touko Aozaki, sister of Aoko Aozaki, appears in this series, and the protagonist, Shiki Ryougi, shares the same abilities as Tsukihime's lead, Shiki Tohno.