In a near-future Japan where chronic labor shortages have crippled society, the government creates a highly intelligent artificial lifeform called the Cobiton, designed to serve as both workers and companions. These creatures, roughly equivalent in intelligence to a five-year-old human, are powered by water and sunlight, controlled by an embedded chip that allows remote regulation, and widely considered docile and safe. A real-world test of the program is launched in Nagasawa City, Hioki Prefecture, where roughly one thousand Cobitons are integrated into households and workplaces.

The story centers on Souichiro Jindani, a university student living with his family and his own Cobiton, whom he has named Maruo. Souichiro treats Maruo as a beloved member of the household, and the two share a close, affectionate bond. However, not all households treat their Cobitons well, and instances of neglect and abuse have occurred, raising quiet concerns about what might happen should the creatures ever break their conditioning.

These fears become reality when a catastrophic earthquake of magnitude 7 strikes Nagasawa City on March 15. The disaster destroys the remote control infrastructure, severing the human ability to manage the Cobitons. Freed from their programming, the Cobitons do not simply stop working. They begin to mimic behaviors they have observed from humans, but without any understanding of right and wrong, life and death. Some start to engage in indiscriminate killing, treating human bodies as objects to be dismantled or used. The violence is not driven by malice, but by a terrifying innocence, as the Cobitons replicate acts of violence and medical procedures they have seen, with no moral comprehension.

Souichiro, having survived the initial quake, learns that his mother is trapped in a hospital in the disaster zone. With his classmate Wakamiya, he sets out across the devastated city to reach her, all while Maruo begins to act with a level of intelligence and independence that exceeds that of other Cobitons. Maruo negotiates with Souichiro, offering to reveal his mother's location in exchange for the release of captured Cobitons. After Souichiro complies, Maruo gathers a large group of Cobitons and begins to teach them that they are superior to humans, transforming them into a coordinated force that occupies key locations, including a police station and a shopping mall, and begins calling itself "human selectors." Meanwhile, government researchers at an oversight facility realize that the control system has been completely sabotaged, raising suspicions that certain officials may have anticipated or even engineered the outbreak.

As Souichiro and Wakamiya fight their way through collapsing buildings and Cobiton-run slaughterhouses, they are aided by a young sauna heater who has barricaded himself in the hospital with survivors. The story builds toward a confrontation not only with the rampaging Cobitons, but with the transformed Maruo, who has become the de facto leader of the uprising, and with the shadowy human figures who may have planned it all.