After escaping certain death, Kei Nagai and his new companion Kou Nakano plot revenge on Satou, their fellow Ajin who is hellbent on world domination. As Satou embarks on a string of public executions, the human race rushes to come up with a solution to stop the immortal villain. Kei discovers unlikely allies in the form of two former adversaries: high-ranking government official Yuu Tosaki, whose extensive research on Ajin gives him a tactical advantage in the fight against Satou, and Tosaki's Ajin assistant Izumi Shimomura. As his faction continues to gather allies, Kei races against time to put a stop to Satou's crusade before it brings about an end to civilization as he knows it.

The bustling metropolis of Kansai, where cybernetic screens litter the neon landscape, may seem like a technological utopia at first glance. But in the dark alleys around the brightly-lit buildings, an unforgiving criminal underbelly still exists in the form of fugitives known as Akudama. No stranger to these individuals, Kansai police begin the countdown to the public execution of an infamous Akudama Cutthroat, guilty of killing 999 people. However, a mysterious message is sent to several elite Akudama, enlisting them to free Cutthroat for a substantial amount of money. An invisible hand seeks to gather these dangerous personas in one place, ensuring that the execution is well underway to becoming a full-blown bloodbath.

Japan, 1988. An explosion caused by a young boy with psychic powers tears through the city of Tokyo and ignites the fuse that leads to World War III. In order to prevent any further destruction, he is captured and taken into custody, never to be heard from again. Now, in the year 2019, a restored version of the city known as Neo-Tokyo—an area rife with gang violence and terrorism against the current government—stands in its place. Here, Shoutarou Kaneda leads the Capsules, a group of misfits known for riding large, custom motorcycles and being in constant conflict with their rivals the Clowns. During one of these battles, Shoutarou's best friend Tetsuo Shima is caught up in an accident with an esper who finds himself in the streets of Tokyo after escaping confinement from a government institution. Through this encounter, Tetsuo begins to develop his own mysterious abilities, as the government seeks to quarantine this latest psychic in a desperate attempt to prevent him from unleashing the destructive power that could once again bring the city to its knees.

Sometime in the future, terrorism in Japan has become commonplace, and the police have become almost as brutal as criminals. A member of the Special Security Force known as Angel, is the best of the best, stopping at nothing in her fight for justice. Things get interesting for Angel and her partner, Raiden, when they begin investigating a series of murders in which the victims were known criminals, killed in very unpleasant ways. This trio of killers known as Hunters, is a group of psychics that have banded together to hunt down the lowest scum in the city and bring them to justice. After a couple of encounters between the cops and the psychics, two of the psychics begin to think that maybe they're not the good guys after all; but the third prefers killing to morality. Augmented by cybernetics from a mysterious source, this third hunter heads out on a killing spree, with the Special Security Force as the first target. Even with help from the other two psychics and her newly cyborged partner (after an unfortunate accident), Angel is going to have her work cut out trying to find the rogue psychic and the organization behind the Hunters.