Inspectors Arata Shindou and Mikhail Kei Ignatov have uncovered a dangerous conspiracy. The Sybil System, the ultimate judge of human character in Japan, is being undermined by a criminal syndicate that is amassing wealth and power in the shadows. Now, Bifrost agent Kouichi Azusawa launches a direct assault upon the Criminal Investigation Department (CID) by occupying its headquarters and taking Inspector Shindou and everyone with him hostage. CID Unit 01 supervisor, along with Chief Mika Shimotsuki and former unit members Shinya Kougami and Nobuchika Ginoza, face the task of reclaiming the building and saving everyone inside. Alongside the hostage situation and Azusawa's demands for Tokyo governor Karina Komiya's resignation, there is a sinister plot hatching in the background—a secret plan that will force Inspector Shindou to confront not only Azusawa but also his own past. These events slowly bring him closer to unshrouding the mystery that has eluded him and his best friend, Ignatov, for many years.

A year and a half after the events of the original sci-fi psychological thriller, Akane Tsunemori continues her work as an inspector—enforcing the Sibyl System's judgments. Joining her are new enforcers and junior inspector Mika Shimotsuki, a young woman blindly and inflexibly loyal to Sibyl. As Akane ponders both the nature of her job and the legitimacy of Sibyl's verdicts, a disturbing new menace emerges. A mysterious figure has discovered a way to control the Crime Coefficient—a number compiled from mental scans that allows Sibyl to gauge psychological health and identify potential criminals. Through these means, he is able to murder an enforcer, leaving behind a cryptic clue: WC? scrawled in blood on a wall. Akane and the rest of Division 01 soon find themselves playing a deadly game against their new foe, coming face-to-face with a conspiracy threatening not only the authority of the Sibyl System, but the very foundation of Akane's own convictions.

Thanks to the Sibyl System, the mental states of society can now be measured on a numerical scale. Using these crime coefficients, a culprit can be apprehended before they ever commit a crime. But is it a perfect system? For Inspectors Kei Mikhail Ignatov and Arata Shindou, that remains to be seen, as their career with the Public Safety Bureau's Crime Investigation Department has only just begun. Shindou and Ignatov are assigned to investigate the crash of a ship carrying immigrants, but they begin to suspect that it was no mere accident. Meanwhile, a mysterious group called Bifrost is observing them from the shadows, but they are not the only ones who have taken an interest in the two new Inspectors.

A runaway vehicle driven by Izumi Yasaka, en route to the Public Safety Bureau building, is reported shortly before it crashes into the building. Izumi is a counselor who recently ran away while working at a latent criminal isolation and rehabilitation facility known as Sanctuary. Before Inspectors Mika Shimotsuki and Akane Tsunemori get to interrogate the suspect, a sudden request is issued from the facility to promptly bring Izumi back. Interpreted as a direct order from the Chief and the board at Sanctuary, the Inspectors obey, but insist that Izumi be escorted back personally. Tsunemori intends to investigate further with the rest of the team at the Bureau. Now Inspector Shimotsuki has finally been given the opportunity she had been waiting for—to be the primary investigator on an important case. This case follows Shimotsuki and her team of Enforcers as they uncover the secrets of Sanctuary.