Five years after the tragic conclusion of the Tokyo Babylon manga, the young head of the Sumeragi onmyoji clan, Subaru Sumeragi, continues his work protecting the people of Tokyo from supernatural threats. Still carrying the emotional scars from the death of his twin sister Hokuto at the hands of the enigmatic assassin Seishiro Sakurazuka, Subaru now investigates a disturbing new case. A man named Kaneyama, a former enemy of the Sumeragi clan, has been found dead. Before his death, Kaneyama had gathered seven teenage girls and taught them the secrets of dark magic, convincing them they are the "Chosen Seven" with a destiny tied to the end of the world. Under his guidance, the girls began using their newfound powers to take revenge on anyone they deem guilty, starting with an abusive teacher. One of the girls, Kurumi, begins to feel remorse for their actions, but the others pressure her to continue with their plans.

As Subaru attempts to intervene and stop the girls from destroying themselves with magic they cannot control, he discovers the truth about Kaneyama's death. The killer is none other than Seishiro Sakurazuka, the Sakurazukamori assassin who murdered Hokuto and who shares a deep, painful history with Subaru. Having disposed of Kaneyama, Seishiro now has no further use for the girls and views them as loose ends to be eliminated. The seven young magic users, suffering from severe side effects caused by their own spells, see Subaru as their enemy and attack him. Subaru finds himself caught between trying to save the girls from their own destructive power and confronting Seishiro, who coldly declares that none of them can be saved.

The tension between the two powerful onmyoji, one sworn to protect life and the other an emotionless killer, finally erupts into a magical duel. As Subaru is pushed to his limits and nearly gives in to his long-suppressed rage and desire for revenge against the man who killed his sister, a supernatural event stops the battle. The spirit of Hokuto Sumeragi briefly manifests, speaking through the body of the remorseful girl Kurumi. Hokuto pleads with both Subaru and Seishiro to stop fighting for her sake. Moved by her intervention, Seishiro withdraws from the confrontation, leaving Subaru alive and their conflict unresolved. In the aftermath, Subaru is left to reflect on the encounter, still haunted by his past and his unresolved, twisted bond with the assassin who remains at large.