In the 41st year of the Shinka Era, on a sunny morning in July, Jirou Hitoyoshi is assigned to secretly observe a confidential meeting between a high-ranking government scientist and an industrial spy. When his cover is blown, it is revealed that the spy is actually a disguised alien. Amid the confusion, Jirou calls upon Kikko Hoshino, a waitress at a café who is also a magical girl, for help—she is part of a society of "superhumans" living hidden among ordinary people, working to defend the Earth from extraterrestrial threats. As an agent of the government's Super Population Research Laboratory, Jirou's job involves protecting superhumans who protect others and neutralizing those who pose excessive risks. Impressed by her competence, Kikko is soon brought into the lab as a new operative.
Five years later, anti-superhuman sentiment and hostility are rising in Tokyo. Problems like governmental corruption, conflicting ideas of justice, and the ethical handling of superhumans have strained the coexistence between humans and the supernatural community, creating uneasy whispers of unrest around the world. For reasons unknown, Jirou has turned against the agency and is now on the run. He moves through the rain-soaked alleys of Shinjuku, evading the very superhumans he once recruited to the cause.