A man and a woman of different ages are killed by a train, their heads crushed in the same gruesome manner. The incident is ruled a bizarre double suicide, but high school student Makoto, whose older brother was one of the victims, refuses to accept that explanation. He soon meets Hoshi Ichi, a young boy who lost his mother in the same event, and the two realize the deaths are connected to a secret organization. As they dig deeper, they uncover the existence of a strange, alien-like entity called SAI, which the organization appears to manipulate. Makoto and Hoshi Ichi become convinced that their relatives were not suicides but were deliberately made to die—possibly through the influence of SAI. The story unfolds over a single summer as the two boys investigate the organization, pursue the truth behind the deaths, and confront the mysterious figure known as SAI's controller, a man named Saitama. Their pursuit leads them to a university professor who once collaborated on SAI research, but just as they close in on the truth, they discover that both Makoto and Hoshi Ichi have been infected by SAI themselves, putting them on the same fatal trajectory as their lost family members. The series resolves with the boys racing to find a way to stop the infection and bring the organization down before they share the same fate.