Sōhei Saikawa, an associate professor of architectural engineering, and Moe Nishinosono, the brilliant daughter of his mentor, travel to a remote island for a university seminar. The island is home to the Magata Research Institute, a secluded facility where the reclusive genius programmer Shiki Magata has lived in isolation for fifteen years. Magata was accused of murdering her parents at the age of fourteen but was found innocent due to her psychological condition, and she has since remained in seclusion, communicating with the outside world only through occasional video conferences. Saikawa, who has long been fascinated by Magata's intellect, and Moe, a mystery novel enthusiast with sharp observational skills, seek to meet her, but their visit coincides with a gruesome and seemingly impossible crime.

The narrative centers on a classic locked-room mystery. The body of Shiki Magata is discovered inside her tightly secured private quarters, a room with no conventional entrance or exit. The corpse is found in a disturbing state, seated in a wedding dress with its limbs severed, positioned on a wheeled cart. Almost immediately after this discovery, Seiji Shindō, the director of the institute and Magata's uncle, is also found murdered. The primary puzzle is how a killer could have entered and escaped from Magata's sealed room, leading Saikawa and Moe into a complex investigation that challenges the boundaries of logic and perception.

As Saikawa and Moe delve deeper, the story moves beyond a simple murder investigation into the dark and twisted psychology of Shiki Magata. Flashbacks reveal her traumatic past, including an abusive relationship with her uncle, and explore her uniquely amoral and detached worldview. The investigation peels back layers of deception, leading to a major revelation: the murdered woman is not Shiki Magata but her secret daughter, Miki. Magata had orchestrated an elaborate plan years in advance to swap identities with her daughter, effectively granting herself a new life while imprisoning the younger woman. The message "Everything Becomes F" is a cryptic clue tied to a programming bug, representing the moment when a system reaches its limit and resets.

The narrative arc follows the intellectual duel between Saikawa and the absent Magata, whose influence permeates every corner of the institute. The climax reveals that Magata murdered her uncle herself to sever the final ties to her past, while the original identity switch was a cold, calculated act to achieve a form of absolute freedom from her own history. The story concludes with Saikawa and Moe confronting the truth, having unraveled a conspiracy that questions the nature of identity, genius, and morality. The resolution leaves the two protagonists to reflect on the enigmatic figure of Shiki Magata, a killer who views murder not as a crime but as a logical step toward personal liberation.