Society was stunned by a case of serial bombings. Raito Shiba, a detective who exclusively handles superhuman cases, gets suspicious that there is nothing left behind at the scene. Raito guesses that employees of the military corporation Yatsuka Heavy Industry were attacked, and investigates the factory in Tachikawa. Then at a nearby park, he meets a girl named Mieko in a schoolgirl uniform. When the conflict worsens with the "Superhuman Bureau," which he has seen as an enemy for long, the surprising secret about Mieko comes to light. Raito, who had his life taken away by an evil organization and was made into a machine body, starts to get complicated feelings in his mind.

Acting against the U.S. which started to use space beasts as a weapon, various countries began to follow suit as to act as a preventative force. Is it possible to peacefully use beasts that can at times become uncontrollable? With the suspicion of the people abounding, the protest movements start to become even more active. The Superhuman Bureau infiltrate Peace University in search of the missing Seiji Matsumoto. However, Jiro gets a mysterious drug injected in him, and he starts to go on a rampage in Equus. Meanwhile, the American army's Space Beast, which was supposed to have been missing, fuses with GaGon and starts a fierce battle.

Housewife Sanae Hatakeyama and her family of six live in the antique shop "Mori-no-ya." Her husband Minoru was the first Japanese prisoner when war broke out with the U.S., and close to 30 years had passed without his return. The seemingly ordinary Hatakeyama family had survived a great disaster that occurred at a nearby chemical plant, and had also been witnessed several times over the years with the exact same family members. Therefore, there were suspicions that they were immortal superhumans. After the Superhuman Bureau gets curious about the family, Fuurouta and the others start on a secret investigation. But then, Sanae receives word that Minoru is returning.

The youth who had awakened to superhuman powers have shifted their sense of justice towards anti-war, anti-America, and anti-establishment, leading them to be called "Superhumanists." Human experimentation and at the Ogasawara Islands and governmental use of superhuman powers come to light. The enraged students rise up for a large-scale protest in Shinjuku, Tokyo in order to realize a "Superhuman Revolution." Jiro gets into action as well, to make Kikko back to normal after she transforms into the queen of the demon world. While Wonder Sword Claude works in stealth, will Jiro be able to follow through with his ideal of "Protect all superhumans"?

A young lady uses musical superpowers to slice and kill aliens lurking on Earth. Her name is Aki Haruka... A former singer for the Angel Stars known as Arachne. The Superhuman Bureau's investigation reveals her to be hiding out in a hospital that is illegally operated by Judas. Then Jiro escapes with Aki in order to protect her from those in pursuit. While on the run, Jiro starts telling Aki a story from two years ago about Rainbow Knight's helmet and a space being called a Fumer.