In the winter of 1995, Mikiya Kokutou passes a young woman during a late night stroll in the snow. Clad in a striking white kimono and bearing an enigmatic gaze, Shiki Ryougi smiles at Mikiya who stares back with curiosity. As they become acquaintances through lunchtime conversations, Shiki begins opening up to him, with Mikiya learning about her unique upbringing.
In September 1998, a string of seemingly random suicides leaves Japan baffled and devastated. But a detective agency specializing in paranormal occurrences notices that there are a few glaring, disturbing similarities tying the deceptively unrelated cases together: All the victims are schoolgirls, and all of them have jumped to their deaths from atop the condemned Fujou Building...
On a solemn night in July 1998, teenager Fujino Asagami is mercilessly raped by a street gang in a dilapidated bar. No matter what physical or sexual abuse they deal, however, the girl regards her captors with the same apathetic expression. The next day, mangled bodies are discovered in that same building, so torn apart that investigators find it infeasible to even consider the culprit human...
Shiki's therapist Touko Aozaki reveals herself to be a magus who is able to perform magecraft. Touko proposes that she can train Shiki to use her newfound eyes: The Mystic Eyes of Death Perception, eyes that can see the concept of death itself. With Touko's assistance, Shiki attempts to fight back against these supernatural beings.
June 1998: After spending two years in a coma caused by a traffic accident, Shiki Ryougi awakens with amnesia. She is visited by Touko Aozaki, a wizard and proprietor of a studio called Garan no Dou. Shiki has lost not only the memory of her accident, but also any real sense that she's even alive. Strangely, enigmatic beings begin to attack her...