In 2113, the Ministry of Foreign Affairs (MFA) dissolved their secret paramilitary unit known as the Peacebreakers. However, the squad disappeared, and their activities remained a mystery. Five years later, the Peacebreakers resurface when they murder Milcia Stronskaya, a scientist in possession of highly classified documents essential to the future of the Sybil System—Japan's surveillance structure that detects potential criminals in society.
To investigate the incident and prepare for a clash against the Peacebreakers in coordination with the MFA, the chief of the Public Safety Bureau decides to recruit the former Enforcer Shinya Kougami back into the force. Having defected years ago, Kougami currently works for the MFA under Frederica Hanashiro's command. Kougami's return creates tensions between him and his former colleagues Akane Tsunemori and Nobuchika Ginoza, but they must set aside their past grudges to focus on ensuring the security of the Sybil System.