Note: for clarity, this retelling follows the events in chronological order, even though the film presents them non-linearly.
In September 1998, taciturn Shiki Ryougi lives alone in a barely-furbished apartment, regularly visited by her close friend, Mikiya Kokutou. One day, he stops by with a small gesture of warmth—strawberry-flavored Häagen-Dazs ice-cream—and their easy banter hints at a comfortable, lived-in friendship. The moment sets a quiet stage for the mysteries to unfold, as Shiki’s world quietly begins to intersect with darker currents.
Shiki’s attention shifts to a perplexing wave of suicides among high school girls. She discusses the cases with the magus Touko Aozaki, the head of Garan no Dou (Hollow Shrine), a detective agency that specializes in paranormal happenings and is staffed by the duo she and Mikiya form part of. What makes these deaths unusual is that none of the victims left a suicide note before leaping from the Fujō Building, a derelict structure slated for demolition. This odd pattern compels Garan no Dou to take a closer look, especially after Mikiya falls into a coma, a state Touko suspects is tied to the suicides.
The investigation takes a supernatural turn when, after locating the corpse of a fourth victim, Shiki witnesses nine ghostly figures hovering above the Fujō Building. She ventures into the building to press the case further and confronts a ghostly presence, suffering grave damage to her prosthetic arm in the process. She recuperates within Garan no Dou while Touko oversees the repairs. When another victim dies and the danger escalates, Shiki returns to the scene for a second confrontation with the apparitions. She ultimately destroys the ghosts using her own extraordinary abilities, though the final specter hurls a chilling curse urging her to kill herself. Shiki remains unfazed and, in a decisive act, defeats the final ghost by stabbing it in the abdomen.
Meanwhile, elsewhere in the city, a terminally ill girl named Kirie Fujou awakens in a hospital bed and is confronted by Touko in person. It is revealed that Kirie has been using her own supernatural power—astral projection and possession—to lure bypassing girls to the Fujō Building to commit suicide. The most powerful ghost is revealed to be Kirie’s astral projection, while the others are the spiritual remnants of the victims. Mikiya’s coma is explained as a consequence of Kirie having possessed him in a bid to draw closer to him. Touko discusses the complex tragedy with Kirie, who confesses that her loneliness and infirmity drove her to lash out in this terrible way by using others. Kirie acknowledges that she has nothing left to live for and expresses a desire to die after witnessing the destruction of her astral projection by Shiki. In the end, Kirie takes her own life at the Fujō Building.
Back at Shiki’s side, Mikiya awakens from his coma with little memory of the events. He returns to Shiki’s apartment, and the two resume their light, teasing banter, ending with Shiki blushing in a moment of shy embarrassment that underscores the fragile, human core of their relationship.
In the post-credits scene, as Azaka Kokutō walks alongside the Fujō Building, Touko remarks that Kirie Fujou probably could not fly that day, hinting at the lingering consequences and the moral weight of the acts that unfolded.