Plot
In January 2118, a Ministry of Foreign Affairs vessel guarding Professor Milicia Stronskaya is attacked by the Peacebreakers, a paramilitary group. One of the operatives, Kai, murders Stronskaya while searching for her research – the Stronskaya papers – before being intercepted by Shinya Kogami, a special investigator for Foreign Affairs's Suppressing Action Department (SAD). Kogami is attacked by a brainwashed SAD agent and fails to stop the Peacebreakers.
In Tokyo, Inspector Akane Tsunemori fights against the proposed dissolution of Japan's Ministry of Justice in light of the Sibyl System's attempts to expand overseas. Both Tsunemori and Atsushi Shindo, chief of the Immigration Bureau, receive word about the Peacebreaker incident and travel to the wrecked vessel. MWPSB Chief Josui Kasei orders Tsunemori to leave the investigation to the SAD, led by agent Frederica Hanashiro and SAD Director Yabuki. Enforcer Sho Hinakawa determines that Stronskaya sent a last-minute message to PSB analyst and Tsunemori's mentor, Joji Saiga.
Saiga tells Tsunemori that Stronskaya's message directed him to a PO box in Dejima. Chief Kasei creates a joint task force with the PSB and SAD to retrieve the Stronskaya papers before the Peacebreakers. Hanashiro tells Tsunemori's team that the Peacebreakers are a Foreign Affairs black-ops unit gone rogue. They are led by Tonami, a fanatical devotee of an unseen "god" he calls The General.
Kogami reunites with Tsunemori and Ginoza, despite heated tensions. Saiga encourages Kogami to apologize to Tsunemori for the illegal actions that led to his exile from Japan, while warning him not resist his violent nature. Kogami makes a half-hearted apology, and Tsunemori warns him that she will arrest him if he breaks the law again.
At the PO box, the team finds a decoy package, and Tsunemori and Kogami realize the operation is a ploy to lure the Peacebreakers out of hiding. The Peacebreakers attack, displaying impossibly low Crime Coefficients, superhuman endurance, and the ability to brainwash SAD agents. Director Yabuki is captured and Saiga is thrown off a ledge to his death. Kai overcomes Kogami after a lengthy skirmish. Instead of killing Kogami, Kai provides subtle clues leading to the Peacebreakers' headquarters and departs.
Kogami and Ginoza go to the Peacebreakers base to rescue Yabuki. They confront Kai, who reveals himself as undercover SAD agent Akira Vasily Ignatov, and returns to Tokyo with them. Akira debriefs Kogami about "the Divider", a cybernetic implant that allows the Peacebreakers to maintain low Crime Coefficients and take control of other SAD agents' implants. Akira reveals he has the Papers and that Professor Stronskaya organized her death to maintain Akira's cover. He explains that Stronskaya's research is the model for a Conflict Coefficient which would allow Sibyl to control warfare and foreign relations. Immediately after the debriefing, Tonami remotely takes control of Yabuki and Akira and attempts to escape, but encounters Shindo. Akira fights off Tonami's control, asks Shindo to look after his brother Kei, and allows Shindo to kill him.
Shindo gives the Papers to the Sibyl System in return for keeping his criminally asymptomatic son, Arata, from being integrated into the system. On the day of Kei's wedding to Maiko, Shindo gives a speech about justice before leaving the reception to commit suicide. Arata later confronts Tsunemori about his father's actions and she encourages him to search for the truth.
Kasei shuts down the investigation, as Sibyl has agreed to give the Peacebreakers the Papers and their own sovereign state on an island in northern Japan in return for them supporting Sibyl's global expansion. Unwilling to let them escape justice, Tsunemori teams up with Kogami, Ginoza, and Hanashiro to raid the Peacebreakers' island. Shimotsuki leads a support team against a Peacebreaker satellite.
Tsunemori goes off alone to face Tonami and the General, which turns out to be a medical AI offshoot of the Sibyl System. Tsunemori is badly injured but uses her Dominator to connect Sibyl to the General, destroying the rogue AI. Tonami prepares to execute Tsunemori, but Kogami arrives and shoots him, leaving Tsunemori distraught.
With the case officially closed, Tsunemori transfers Ginoza and Sugo to the SAD while the Sibyl System promotes her to a senior role within the Ministry of Welfare. Disillusioned, Tsunemori sends a letter to Kogami, revealing her intentions to challenge Sibyl's control of the justice system. At her inauguration ceremony, Tsunemori shoots Chief Kasei while maintaining a low Crime Coefficient, which should be impossible under Sibyl. Plans to expand Sibyl's realm of influence are put on hold, and Tsunemori is taken into custody, with Kogami resolving to free her.
