The narrative is defined by major plot twists across each season:
- Season 1: Atsushi discovers that the rampaging white tiger is his own untamed ability rather than an external beast. Dazai intentionally orchestrates his own capture by the Port Mafia to gather intelligence on the Guild’s bounty on Atsushi.
- Season 2: Port Mafia Boss Ōgai Mori intentionally engineered the deaths of Sakunosuke Oda’s foster orphans to force Oda into a suicidal mutual kill with Mimic leader André Gide, thereby securing the government's Special Ability Business Permit. During the Guild climax, Atsushi and Akutagawa unite aboard the crashing Moby Dick, and Kyōka passes her Agency entrance test by sacrificing a drone to save the city.
- Season 3: Fyodor Dostoevsky infects Fukuzawa and Mori with the Cannibalism virus. Dazai and Ranpo outmaneuver him by using Natsume Sōseki (disguised for years as the calico cat Sensei) to broker peace, capturing Fyodor.
- Seasons 4 & 5: The Decay of the Angel uses a page from The Book to frame the Agency as terrorists. Their leader, Kamui, is revealed to be Ōchi Fukuchi—Fukuzawa’s childhood friend and commander of the Hunting Dogs. Fukuchi uses Bram Stoker's virus to create a global vampire army. In Meursault prison, Chūya's vampirism is revealed to be a ruse; using gravity manipulation to stop bullets, Chūya and Dazai engineer the destruction of Fyodor's escape helicopter. Fukuchi's scheme is revealed as a gambit to unify world superpowers against a common threat to avert a catastrophic world war, accepting death to pass the defense mantle to Fukuzawa before a flash-forward reveals a new cosmic threat.