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.