In the 41st year of the Shinka Era, on a bright July day, Jirou Hitoyoshi is assigned to secretly eavesdrop on a confidential meeting between a high-ranking government scientist and an industrial spy. But his cover is blown, and the spy turns out to be an alien in disguise. During the ensuing commotion, Jirou calls on café waitress and magical girl Kikko Hoshino for help—she is one of many "superhumans" living hidden within society, quietly protecting humanity from extraterrestrial dangers. As an agent of the government's Super Population Research Laboratory, Jirou's job is twofold: safeguard superhumans who defend people, and eliminate those considered too hazardous to exist. After proving herself a reliable ally, Kikko is invited to join the agency as its newest member.
Five years later, disapproval and hostility toward superhumans have become widespread in Tokyo. Between government corruption, clashing ideas of justice, and the ethics of superhuman rights, the balance between humans and the supernatural minority is fragile, with whispers of unrest and unease spreading throughout the world. Under mysterious circumstances, Jirou has betrayed the agency and is now a fugitive on the run. As he sneaks through the rainy back alleys of Shinjuku, he is chased by the very same superhumans he once recruited.