It is the 40s of the Shinka Era... In Japan, "superhumans" such as giant aliens, super robots, and monsters were active. While causing mysterious incidents, the "superhumans" at times stop destruction and save people. Jiro Hitoyoshi belongs to the "Superhuman Bureau," which works to register and protect such superhumans, and he has come to scout Kikko Hoshino, who is working as a server at a café. She is a "witch girl" type superhuman. And right in front of Jiro and Kikko, a battle between Grosse Augen, the superhuman of justice, and an "S" Planetarian unfolds, leaving Jiro and Kikko no choice but to join in the battle.
While working as a waitress at a cafe, Kikko Hoshino is asked by a man named Jiro Hitoyoshi to do a job for him, preventing a top Japanese scientist named Professor Onda from selling research secrets to a corporate spy. Strangely enough, on the day of the deal, the supposed spy is seen giving Onda a package instead of taking one from him. Even so, Kikko stops Onda from leaving, as the spy reveals himself to be an alien from Planet S. Kikko reveals herself to be a magical girl, and teleports outside with the package. However, the alien follows and grows giant-size until the giant superhuman Grosse Augen appears and vanishes with the alien. With Kikko and Jiro's help, Grosse Augen defeats the alien, but Jiro tracks down his alter-ego anyway and confronts him. Grosse Augen turns out to be an alien borrowing a Japanese policeman's body as it would have died otherwise, but the strain is supposedly killing them both. Jiro appears to take Grosse Augen into an alleyway and vaporize him.
The scene flashes to a point five years later, where Jiro managed to help the alien Grosse Augen reach his home planet and revive the policeman in the body of the defeated S Planetarian. As a result, the Superhuman Bureau made Jiro a target, and he refuses to go with Kikko as he escapes with the policeman.