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. Jirou 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 Jirou and Kikko, a battle between Grosse Augen, the superhuman of justice, and an "S" Planetarian unfolds, leaving Jirou and Kikko no choice but to join in the battle.

Fuurouta is a prank-loving ghost with transformation abilities. He became a bird at a department store in Ginza and let free a beautiful insect that was on sale. However, it was no average insect at all. The "Black Fog" that occurred at the same time flowed to Nagatacho and engulfed the area around the National Diet Building. Jirou and Kikko, who were handling the problem, meet Fuurouta at the police station and take him to the "Superhuman Bureau." Fuurouta gets interested in the bureau's activities and tries to go against the "Black Fog" in order to join...

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.

A month has passed after superhuman Grosse Augen, who has fought beasts, left Earth. And as if they were waiting for this moment, beasts appear one after another. Since a number of superhumans new and old, like Human Satellite Robot Earth-chan, fought together, each incident was solved before there was any large damage. With a beast craze going on, Jiro visits a company trying to start a radio exclusively for beasts. There, he witnesses the small beast GaGon, who is friendly with humans. What sort of secret lies in the beast that is controlled by evil and goes wild?

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.

The popular novelty band "Mountain Horses"... When "The Quartet" came to Japan and sold out the Nippon Budokan in June, the 41st of Shinka Era, they were playing as the opening band. Once the concert starts, the souls of the young people become liberated by the power of music. Is that the superhuman power that "The Quartet" has? Each of the Mountain Horses members who came into contact with them gain supernatural powers, but they were only usable for comedic purposes. Eventually, a conspiracy starts to progress, revolving around the superhuman powers that started to appear among the young people.

Superhuman Judas, or Hikaru Misumi, was part of the armed robbery group Diamond Eater, but had a change of heart after being defeated by Human Satellite Earth-chan. After being released from prison, Hikaru is registered in the Superhuman Bureau, and decides to protect the activities of young people like him. However, the extreme actions of Earth-chan, who reacts to the brain waves of people calling for help, become recognized by society as absolute justice. During the student protest at Haneda Airport against Japan's participation in the Earth Defense Corps, Earth-chan appears while she is guarding the Prime Minister.

The Secret Detective Team BL led by Yumihiko Otonashi refuses superhuman registration and has continued to act on their own with a massive robot named Gigander Seven. Then, Yumihiko receives a notice saying the evil superhuman Lucifer's Eyes will steal superhuman Rainbow Knight's "Crescent Gun" from a collector. Rainbow Knight is a popular superhuman who gave hope to Japan after the war, and Jiro too holds dearly an experience where he was saved by Rainbow Knight. However, Rainbow Knight, the hero of justice, has been labeled as the culprit of the "Otetsu Kidnapping," and there was a conspiracy theory regarding the death involved...

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.

Infernal Queen is a fanatical organization that ruthlessly kills everyone from politicians to criminals if deemed evil by the organization. Their scientifically almighty mothership IQ has flown from the American continent to Japan, where the Superhuman Bureau is, and started executing criminals. Suspicion is placed on Hyouma as he looks like the leader of IQ, and the masked Public Security Force Chief Shakko comes to the Superhuman Bureau. Are the same two people existing at the same time? Hidden behind the mystery was the secret of Jaguar, or Hyouma, that absolutely cannot be shared with others.

Along with the return of the Ogasawara Islands, the U.S. Navy's state-of-the-art submarine Antares will be coming to Yokosuka. Students flock to the port in order to see the show by the popular group "Angel Stars." Then radical superhumans hiding amongst the crowd start to protest, and there is chaos after musical notes materialize in sync with the performance. And then, a superhuman calling himself Wonder Sword Claude slices the submarine in half and starts to uncover the terrifying secret hidden inside Antares.

Murders targeting doctors and nurses have taken place in Sapporo. During the investigation of SPR children who manipulate magic and science, it is revealed that superhumans are used as guinea pigs for a horrible experiment. What is the goal of Wonder Sword Claude who is suspected as the mastermind? Kikko visits the Municipal Hakko High School when the heroic superhuman Galboi Riker who flew from the Soviet comes falling down in a horrid state. The students get a testimony saying he was shot down by the Self-Defense Force and the American superhuman Master Ultima, and rise up against the tyranny of the government.

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"?

In the aftermath of the Shinjuku student protests, the government comes to view superhumans who are not under their supervision as nothing but gangs of dangerous criminals. The Public Security Force is strengthened with the installation of giant robots. It places the Superhuman Bureau along with Raito and the others, minus Jiro who has left, under their control and enforces training to keep peace and order. An android warrior calling himself Yusei Washizu arrives in a UFO. He is a messenger sent by a peace alliance of intelligent lifeforms in outer space, and has come to Earth to capture an S-Planetarian who has caused the exinction of many star systems.

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.

The Winter International Sports GP in Sapporo is just a month away, and gaining popularity are the three superhumans who had received body modification surgery for the ski jump: the Three Birdmen. However, the three are struck by lightning from a mysterious black cloud and get monstrous beings resembling flowers on their heads. Now it is questionable if they can even participate in the exhibition jump. Another jumper, Amato, is suspected as the culprit as he was feuding with the three for refusing the superhuman surgery. But the black cloud just keeps growing and its lightning strikes more and more innocent civilians...

Winter, the 47th of Shinka Era... Fire breaks out on an overnight express train in the Hokuriku region tunnel. Upon hearing the news, Emi heads to the deep underground to meet Devila, a female Yokai known for hating humans. Devila's tribe is at an equal rank as Emi, and Emi feared that Devila had sent out a warning to humans for reaching the deep underground with the Shield Method. Meanwhile, Devila's younger brother Devilo appears in Shinjuku, looking exactly like a human. His poetic and meaningful words start to move the souls of those passing by...

The Canada Goldenrod, a non-native plant, rapidly grows in many areas all over Japan. Wakamura seems to be allergic to the pollen, but he soon finds out there is more to this plant than the sneezing.

A superhuman is discovered, still alive, in a block of ice. She is Koma, the legendary Iron Mask Fencer from the Sengoku period of Japan.

War has changed Master Sergeant Jonathan Morrell. Trying to escape the horrible memories of the atrocities he experienced, Jonathan goes AWOL. The Superhuman Bureau must work with the U.S. military to track him down.

Three "super robots" are imported to Japan as part of a new project for public safety. Raito and Aki attack one of the robots during transit, but neither their attack nor the super robot project goes as planned.

A new movie is released in Japan, instantly filling theaters. The movie stars lookalikes of the Superhuman Bureau, and claims to reveal a hidden truth.

The Superhuman Bureau is officially disbanded, and its former members either go into hiding or join the government. Then, Master Ultima hosts the Okinawa Superhuman Expo, a major event showcasing the benefits that superhumans possess.

Superhumans are now divided into two groups, and every superhuman is forced to choose a side. Jirou, as a beast, leads the war against humans, and now Kikko must face him—all according to Satomi's plan.