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...

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.

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...

Upon investigation, Mikiya finds information on Fujino's past, leading him and Touko to deduce a possibility behind Fujino's chronic pain and supernatural powers. As Mikiya and Touko race against time, Shiki and Fujino confront each other again face to face.

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...

Shiki reaches the rooptop of the abandoned Fujou building to confront the source of the recent string of suicides to not only put an end to the suicides but to also bring Mikiya's consciousness back. Touko meanwhile goes to meet the culprit behind the suicide incidents.

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.

When Mikiya notices possible connections between Shiki's injuries and information about the murders, he begins to monitor Shiki's activities. However, his concern for Shiki's safety may bring him more danger than he initially expected.

In February 1999, a string of murders has Shiki Ryougi and Mikiya Kokutou on edge. These crimes share a disturbing resemblance to a similar set of homicides from 1995, when Shiki and Mikiya first met, and awaken a dark, murderous desire that has laid dormant within Shiki's soul ever since then.

After connecting the dots, Mikiya arrives at an apartment that eerily has numerous pictures of Shiki pinned across the walls. Mikiya comes across a diary on a nearby table detailing the writer's unnatural obsession with Shiki. As he reads the entries however, someone enters the room.

Shiki and Lio Shirazumi confront each other, but when Lio tempts Shiki into killing him, Shiki is suddenly reminded of the events three years ago that she had forgotten in the accident.

When Shiki tries to leave, Lio reveals to her that he had just killed Mikiya "for her sake," which puts Shiki into a state of distraught. As Lio makes his way to attack her, Shiki finally comes to terms with her thoughts and feelings.