While attending a meeting as a Chief Inspector of the Public Security Bureau, Akane Tsunemori received a report that an incident had occurred on a foreign vessel , and this was the beginning of a big and unexpected case.

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. Just what do the girl who wishes for revenge and the man who has exacted revenge see as they gaze upon the edge of a world from which there is no escape?

In the winter of 2117, 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.

2112; the summer before Akane Tsunemori was assigned to Division One of the Public Safety Bureau’s Criminal Investigation Department. Teppei Sugo, an accomplished pilot of the Defense Army’s 15th Integrated Task Force, 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 of CID Division One is dispatched to Sugo’s military base to investigate the truth behind this case.

Year 2116—The Japanese government begins to export the Sibyl System unmanned drone robots to troubled countries, and the system spreads throughout the world. A state in the midst of a civil war, SEAUn (the South East Asia Union), brings in the Sibyl System as an experiment. Under the new system, the coastal town of Shambala Float achieves temporary peace and safety. But then SEAUn sends terrorists to Japan. They slip through the Sibyl System and then attack from within. The shadow of a certain man falls on this incident. In charge of the police, Tsunemori travels to Shambala Float to investigate. The truth of justice on this new ground will become clear.

Tokyo, Winter. Despite the use of the Youth Ordinance Bill to enforce curfews for minors and regulate the use of the Internet, young people continue to fight for their own freedom through underground methods. One such group calls themselves Surat. They have decided to take on Fumito Nanahara, a man who has great influence on the political world, and basically controls Tokyo with an iron fist. While using the Internet as a weapon to discover more information about Fumito, they learn about “Tower”, the secret organization behind Fumito which engages in human experimentation.