In an alternate version of Japan, superhumans from all different forms of fiction now coexist with humans: witches, kaiju, cyborgs, and even youkai. Some use their powers for criminal acts, some use them for heroic acts, and some even use them to just live normal lives. With the introduction of these new superhumans, the Japanese government formed the Superhuman Bureau: a team of individuals who overlook and protect them. The story follows Jiro Hitoyoshi, a member of this bureau, and what his grand purpose really is in all of this. Is what he's doing with the bureau good or is he no better than the criminal superhumans he keeps in check?

January 1999: Apprentice mage Azaka Kokutou, Mikiya's younger sister, has been ordered by her mentor, Touko Aozaki, to investigate a certain incident in which fairies steal the memories of students at Azaka's school, Reien Academy. Azaka launches an investigation with the help of Shiki.

In February 1999, a string of murders has Shiki Ryougi and Mikiya Kokutou on edge. These crimes share a disturbing resemblance to a similar set of homicides from 1995, when Shiki and Mikiya first met, and awaken a dark, murderous desire that has laid dormant within Shiki's soul ever since then.

2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a "Cosmo Reverse System" at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the "Gatlantis," and that its leader is the Gutaba expeditionary force commander who calls himself "Goran Dagaamu of Thunder." The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the "Flame Direct Attack Cannon" that can transcend space.

Ajin is a live-action adaptation of a Japanese manga series written and illustrated by Gamon Sakurai. Kei Nagai dies in a car accident, but realises he is a type of immortal known as Ajin (demi-human). Hunted by humans, Ajin is eventually found by the government and used as a subject in cruel experiments. He finds fellow demi-humans along the way as he escapes and goes on the run.

The silver-haired samurai Sakata Gintoki investigates the disappearance of a legendary sword named Benizakura while his partners Kagura and Shimura Shinpachi try to find out what has happened to Gintoki's friend, Kotaro Katsura.