Tatsumi Sekiguchi reads part of a transcript, titled "The Woman inside the Box" by Shunkō Kubo; and imagines himself as the story's protagonist. In it, he is traveling to his grandmother's funeral on a train with another man, who possessed a box containing the live head of a girl. In the main storyline, Kanako Yuzuki chooses classmate Yoriko Kusumoto to be her friend. Yoriko's mother, Kimie, believes Yoriko has been influenced by a mōryō, an evil spirit, when Yoriko begins taking nighttime strolls with Kanako. Kanako and Yoriko plan to go to Lake Sagami over summer break. On the night they leave, Yoriko witnesses Kanako crying, as well as a pimple on the back of her neck; both points perplex Yoriko. Soon after, Kanako is hit by the train on which detective Shutarō Kiba is traveling.

Sekiguchi reads more of "The Woman inside the Box," imagining himself as the protagonist. In it, he attends his grandmother's burial. Afterward, he continues to think about the girl in the box. In the main storyline, Kiba fails to get a coherent statement from Yoriko. Constable Fukumoto takes him and Yoriko to the hospital treating Kanako. Once there, Noriyuki Masuoka, Noritada Amemiya, and Yōko Yuzuki also arrive. Kiba and Fukumoto recognize Yōko as the former actress Kinuko Minami. After the hospital stabilizes Kanako, Yōko has her transferred to Kōshirō Mimasaka's hospital. Several days later, the discovery of a severed arm and two boxed, severed legs catches the attention of Morihiko Toriguchi, who travels with Atsuko Chūzenji and Sekiguchi to investigate. While driving around lost, they stumble upon Mimasaka's hospital.

Kiba thinks about the events of the last few days. In a non-linear flashback, Fukumoto escorts the transfer of Kanako to Mimasaka's hospital, a virtually-windowless box-like building in the middle of a forest. This facility is staffed by only two doctors, Mimasaka himself and Tarō Suzaki, as well as a maintenance engineer. Meanwhile, Kimie has become even more convinced that Yoriko is possessed. She brings Hyōei Terada to her house. He performs an exorcism of the house, and tells her that she can purify herself by giving him her tainted material wealth. Yoriko tells Kiba that Kanako was pushed by a man wearing gloves. Kanako disappears from the hospital, and Kiba later discovers Yōko with a ransom note in her hand.

Sekiguchi reads more of "The Woman inside the Box", imagining himself as the protagonist. In it, he dismembers girls and wonders why he is unable to keep their heads alive. He resolves to meet the doctor that kept the girl alive in the box. In the main storyline, Kiba continues his flashback. Yōko asks Kiba to investigate, despite the Kanagawa police having jurisdiction. Later, Suzaki is found murdered, and Amemiya disappears. Back in the present, Sekiguchi's editor asks him to review a manuscript from Shunkō Kubo. A gloved man dismembers a prostitute. After Kiba is suspended from the Tokyo police, Bunzō Aoki asks him for help on the Musashino dismemberment case and Kanako's kidnapping. Kiba investigates Yōko and discovers that, during her film career, she was stalked by someone matching Suzaki's description. Kiba also investigates Mimasaka and discovers that he researched the creation of artificial, immortal soldiers during the war.

Sekiguchi reads a section of his own work titled "Vertigo" and imagines himself as the story's protagonist. In it, he pursues a woman through a large, empty house. In the main storyline, a flashback to 1880 recounts scholars testing Ikuko Nagao and Chizuko Mifune for clairvoyance. In 1911, they test Ikuko for psychic photography. One of the scholars reports to the press that clairvoyance is fake. Back in the present, Masuoka hires Reijirō Enokizu to find Kanako. Masuoka explains that Hiroya Shibata, the only heir to the fortune of Yōkō Shibata, eloped with Yōko Yuzuki before she became an actress. She later gave birth to Kanako. Yōkō agreed to fund all expenses for raising Kanako under the condition that Kanako must never know her true parentage. Amemiya was appointed to monitor that condition. After Hiroya died during the war, Kanako became Yōkō's heir, and Yōkō recently died. Sekiguchi introduces Toriguchi to Akihiko Chūzenji.

Atsuko interviews several kids in the area of the crimes. They all report seeing a man in dark clothes with white gloves. Sekiguchi and Toriguchi continue to meet with Chūzenji. Chūzenji describes the differences among espers, diviners, mediums, and priests. In particular, he cautions that people can mistakenly follow mediums as if they were prophets of a religion, but religions are organized by the believers, not the leaders. Toriguchi relates how he obtained a list of believers in a new religion. The list is labeled "Onbako-sama," but Onbako-sama is the name of a box that Hyōei Terada, the leader, has. Previously Terada was a box-maker. Onbako-sama is the source of his spiritual power. Furthermore, Terada's grandmother had a spiritual power that scholars tried to study. She left a box, inside which was a tin vase containing a piece of paper with the word "mōryō" written on it. Terada began gathering religious followers when he discovered the box in an attic after the war.

Sekiguchi reads more of "The Woman inside the Box," imagining himself as the protagonist. In it, he remembers being alone is the large house where he grew up. In the main storyline, Sekiguchi and Toriguchi continue to meet with Chūzenji. Toriguchi relates that the teachings of Onbako-sama are that mōryō gather in places that are enclosed. Chūzenji says that Terada has grasped the basic nature of mōryō. Toriguchi explains further that Terada convinces his followers that they must part from their impure materialism. Toriguchi wants to expose Terada as a criminal and believes Terada is involved with the dismemberment case, because all the victims are daughters of followers listed in the Onbako-sama membership registry. Sekiguchi notices that Shunkō Kubo is on the list of followers. Sekiguchi reads more of "The Woman inside the Box," imagining himself as the protagonist. In it, he sells the large house and rents a single room. He proceeds to fill the room with custom-made boxes.

Sekiguchi reads more of "The Woman inside the Box," imagining himself as the protagonist. In it, he finishes filling his room with boxes when he receives notice of his grandmother's death. He takes a train to his grandmother's funeral and finds himself sitting with the man who has a box. In the main storyline, Sekiguchi gives a copy of the Onbako-sama registry to Satomura, the coroner in the dismemberment case. Satomura gives it to Kiba to give to Aoki. Sekiguchi, Toriguchi, and Enokizu meet with Chūzenji. Sekiguchi notices that Yoriko's mother is on the Onbako-sama list. Kiba arrives and overhears Enokizu telling the group that Yōko is Kanako's mother, not her sister. Chūzenji suggests Kiba and they share information. Yoriko finds herself locked out of her house as Enokizu and Sekiguchi arrive to talk to her. She excuses herself to meet the gloved man, who tells her he thinks he knows where Kanako is. The gloved man takes Yoriko to an abandoned temple filled with boxes.

Shunkō Kubo is the gloved man. "The Woman inside the Box" is more a diary than a work of fiction. In flashback, Enokizu and Sekiguchi are on their way to talk to Yoriko. Sekiguchi notices he forgot his copy of "The Woman inside the Box" at Chūzenji's. When they meet Kubo by chance in a cafe, they show him Kanako's picture. He is shaken and says he might be able to help find her. After they meet Yoriko and she leaves to meet Kubo, they break into Yoriko's house to find her mother attempting suicide. They tell her that she must protect Yoriko if she returns. Rejoining the timeline, Yōko tells Kiba that Mimasaka tried to cure her mother's myasthenia. Chūzenji has read "The Woman inside the Box." After Sekiguchi tells him that Kubo wears gloves, he deduces that Kubo is the perpetrator of the dismemberment case. Aoki stops by to say that Yoriko's severed arms have just been found.

A priest seals peoples' worries in stone shrines. The ascetic tries to stop it, but ends up joining the priest. Chūzenji believes the story is autobiographical and indicates Kubo is the ringleader behind Onbako-sama. Chūzenji, Sekiguchi, and Enokizu go to confront Terada. Chūzenji says that the box with a tin vase containing the written word "mōryō" was a clairvoyance test for Ikuko Nagao and that Onbako-sama is an iron box that contains the fingers of the man behind Terada. After Chūzenji demonstrates that all of Terada's practices are fake, Terada confesses the swindle to the police and reveals that Kubo is his son. Afterward, Chūzenji tells Sekiguchi and Toriguchi that he knew Yoriko would be the next victim because Kubo just went through the Onbako-sama register alphabetically. Meanwhile, Aoki goes to the abandoned shrine Kubo is using, but Kubo escapes by force. Aoki, injured in Kubo's flight, finds and opens the box containing Yoriko's head. Later, Kubo's severed limbs are found.

On the way to visit Aoki, Chūzenji tells Sekiguchi, Toriguchi, and Enokizu that he worked with Mimasaka during the war, although on a different project. Mimasaka researched replacing biological human body parts with mechanical ones to create soldiers who could not be killed. The only personal information Chūzenji ever learned about Mimasaka is that his wife's name was Kinuko. In a flashback, Kiba tells Yōko that he knows she is Kanako's mother. Yōko tells Kiba that she intends to claim Kanako's inheritance to pay for Kanako's medical care. In the present, Kiba goes to Mimasaka's hospital to confront him. Sekiguchi, Toriguchi, and Enokizu pick up Yōko and go to stop Kiba. Kiba accuses Mimasaka of dismembering girls to further his research, and demands to know what he has done with Kanako.

Sekiguchi reads a section of his own work, titled "Vertigo", and imagines himself as the story's protagonist. Sekiguchi, Toriguchi, Enokizu, and Yōko arrive in time to stop Kiba from killing Mimasaka. Yōko reveals that Mimasaka is her father, and Enokizu hits the stunned Kiba for his foolishness. Chūzenji begins recounting the series of events, beginning with Yoriko pushing Kanako onto the train tracks, then reporting a perpetrator based on the assassin in Sekiguchi's "Vertigo." Mimasaka could only keep Kanako alive mechanically—a very expensive treatment. Suzaki had been blackmailing Yōko, because he knew that Hiroya Shibata and Yōko conspired to make it look like Kanako was Hiroya's child, but Yōko was already pregnant when they met. Since only Kanako's head remained alive, it would have been easy to stage her kidnapping and demand a ransom from Yōkō Shibata. In the present, Chūzenji confirms that Mimasaka is keeping Kubo's head alive, using the "hospital" as a mechanical human body.

Chūzenji continues recounting the series of events. The first severed limbs found, before Kanako's abduction, were Kanako's. After Suzaki took Kanako's head, Amemiya killed Suzaki and ran away with the head. Kubo met Amemiya on a train and saw Kanako's head alive inside the box. Kubo tried to keep the heads of other girls alive in a box for himself. Before he killed Yoriko, she told him about Mimasaka. Kubo wrote about it in "The Woman inside the Box", then went to Mimasaka, who performed the same procedure on Kubo. Mimasaka's project of implanting a human brain into a machine began when he tried to treat Kinuko's myasthenia. Mimasaka treated Kubo as simply another research subject. When the police try to arrest Mimasaka for what he did to Kubo, he grabs the box with Kubo's head and tries to escape with Yōko. Kubo bites Mimasaka in the neck and kills him, leading Yōko to kill Kubo. Kiba arrests Yōko for the murder of Kubo.