The story takes place between August and October, 1952. It primarily follows crime fiction writer Tatsumi Sekiguchi and news magazine editor Morihiko Toriguchi as they investigate, with the help of onmyōji Akihiko Chūzenji, a series of unusual crimes that take place in Musashino and Mitaka.

Kanako Yuzuki and Yoriko Kusumoto are friends and middle school students. Kanako and Yoriko plan to go to Lake Sagami over summer break. On the night they leave, Kanako is hit by the train on which Tokyo police detective Shutarō Kiba is traveling. After the hospital stabilizes Kanako, Yōko Yuzuki, Kanako's older sister, has Kanako transferred to Kōshirō Mimasaka's research hospital. Several days later, the discovery of a severed arm and two boxed, severed legs is what catches the attention of Toriguchi, who travels by automobile with Atsuko Chūzenji and Sekiguchi to investigate.

Yoriko tells Kiba that Kanako was pushed by a man wearing gloves. Shortly afterward, Kanako is apparently abducted from the hospital; Mimasaka's assistant, Tarō Suzaki, is murdered; and Kanako's guardian, Noritada Amemiya, also disappears. Witnesses report seeing a gloved man in the area where three other girls are soon abducted. Residents of the surrounding area later discover the girls' boxed, severed limbs.

Noriyuki Masuoka, the lawyer for Kanako's grandfather, hires private investigator Reijirō Enokizu to find Kanako. Masuoka explains that Yōko is Kanako's mother, not her sister. Kanako is unaware of her true parentage, but she is the only heir to the fortune of Yōkō Shibata, who appointed Amemiya as her guardian.

Toriguchi obtains a list, labeled "Onbako-sama", of believers in a local cult led by Hyōei Terada, a self-proclaimed onmyōji. Toriguchi believes Terada is involved with the dismemberment case, because all the dismemberment victims are daughters of Terada's followers. Sekiguchi notices that both Yoriko's mother and fiction writer Shunkō Kubo are on the Onbako-sama list. As a fellow writer for the same publisher, Sekiguchi already knows Kubo, who always wears gloves. After Enokizu and Sekiguchi meet with Yoriko, she meets Kubo, who takes her to an abandoned temple filled with boxes. Later, Yoriko's severed arms are found.

From reading Kubo's latest fiction work, Chūzenji deduces that Kubo is the perpetrator of the dismemberment case. Chūzenji, Sekiguchi, and Enokizu confront Terada and demonstrate that all of Terada's practices are fake. Terada confesses his swindle to the police and reveals that Kubo is his son. Meanwhile, Tokyo police detective Bunzō Aoki goes to the abandoned temple that Kubo is using, but Kubo escapes. Later, Kubo's severed limbs are found.

Chūzenji tells Sekiguchi, Toriguchi, and Enokizu that he knew Mimasaka during the war. Mimasaka's research involved replacing biological human body parts with mechanical ones. Meanwhile, Kiba accuses Mimasaka of dismembering girls to further his research and demands to know what he has done with Kanako. Sekiguchi, Toriguchi, and Enokizu pick up Yōko and arrive at Mimasaka's facility. Yōko tells them Mimasaka is her father. Chūzenji soon arrives with Masuoka, Aoki, and police constable Fukumoto.

Chūzenji recounts the series of events, beginning with Yoriko pushing Kanako onto the train tracks. Suzaki had been blackmailing Yōko, because he knew that Kanako was not Yōkō Shibata's legitimate heir. Since Mimasaka could keep only Kanako's head alive mechanically, Suzaki could easily stage her kidnapping and demand a ransom from Shibata. 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 Kanako's head. Kubo met Amemiya on a train and saw Kanako's head alive inside a box. Kubo himself then tried to keep the heads of other girls alive in a box. Kubo wrote about it all in his fiction. Before he killed Yoriko, she told him about Mimasaka. When he went to Mimasaka, Mimasaka performed the same procedure on Kubo.

Aoki tries to arrest Mimasaka for what he did to Kubo, but Mimasaka grabs the box with Kubo's head and tries to escape with Yōko. Kubo bites Mimasaka in the neck and kills him, so Yōko kills Kubo. Kiba arrests Yōko for the murder of Kubo.