Season 1: Akane and Kogami pursue Makishima, whom the Dominator cannot read because his Crime Coefficient never rises. Kogami is taken off the case because Sibyl does not want Makishima dead. Akane's friend is used as bait in the subway episode. Akane is later offered a deal by Sibyl, which she accepts without surrendering her convictions. In the end Kogami kills Makishima and leaves Japan, while Sibyl remains intact and Akane remains an Inspector.
Season 2: A new villain, Kirito Kamui, is revealed as a collective mind of seven people who can cloud Psycho-Passes by speaking with people. Several characters die, including Inspector Aoyanagi, members of Division 3, and Akane's grandmother. At the climax Akane leads him to Sibyl's core, and Sibyl chooses to recognize him as one of its own.
Season 3: The story moves to an international stage, with Bifrost, a criminal organization that uses an AI to predict real-world outcomes for gambling, and Sibyl spreading beyond Japan. Kogami returns with further depth in characterization.