Following the incident in the Southeast Asia Union in 2116, Shinya Kogami resumes his vagrant journey. In a small South Asian nation, Kogami rescues a bus of refugees under attack by armed guerrilla forces. Among the refugees is a young lady by the name of Tenzin, who begs Kogami to teach her how to retaliate against the enemy.

2112; the summer before Akane Tsunemori was assigned to Criminal Investigation Department. Teppei Sugo, an accomplished pilot of the Defense Army, joins the military operation in Okinawa. Three months later, an unmanned combat drone opens fire on the Ministry of Defense in Tokyo. Enforcer Tomomi Masaoka is dispatched to Sugo's military base to investigate the truth behind this case.

A runaway vehicle crashes into the Public Safety Bureau Building. The driver is identified as Izumi Yasaka, a psychological counselor at the Sanctuary, a Latent Criminal Isolation Facility in Aomori Prefecture. But right before her interrogation, Inspector Mika Shimotsuki and Enforcer Nobuchika Ginoza are tasked with promptly escorting Yasaka back to Aomori. What awaits them there is a False Paradise.

Acreditando na humanidade e na ordem, a polícia Akane obedece ao sistema informático Sibyl. Mas quando se depara com um mestre do crime que pode iludir este sistema "perfeito", ela questiona tanto Sibyl quanto ela mesma.