In the future, people's minds are analyzed to determine their criminal potential. New Inspector Akane Tsunemori learns first-hand what it means to be an Inspector as she starts her job off with a difficult case.

The CID is brought in to investigate a series of deaths caused by Drones at a Drone manufacturing plant, as well as a mysterious disappearance. Akane becomes intrigued and also stumped by the behavior of Kogami, one of the Enforcers.

The CID's investigations into the recent murders lead them to suspect that a highly skilled hacker is assisting the killers. Kogami starts to see similarities between the current cases and the case where his colleague Sasayama was murdered.

Ginoza decides to take Kogami off the current case since it is eerily similar to the case of Kogami's subordinate's murder. Meanwhile, Kogami and Akane investigate independently, which leads them to conclude that the killer is within Ousou Academy.

Rikako Ouryou's case finally gives the CID a solid lead on Makishima and they begin investigating to learn more about him. In the meantime, Kogami takes Akane to have her meet a professor who used to give lectures at the MWPSB.

After Kogami was finally able to contact his CID team, he and Yuki try to stay alive as Senguji hunts them. While responding to Kogami's request for reinforcements, Akane comes face to face with the ringleader behind the kidnapping of her friend Yuki.

By undergoing a Memory Scoop, Akane was able to help the CID generate a photofit picture of Makishima. While they try to track down Makishima, he starts a new crime using a device that can deceive the Sibyl System's security.

Riots break out when people are given helmets that allow them to avoid detection by the street scanners, throwing the city into chaos. The MWPSB must quell the riots while also dealing with citizens who are fighting back against the rioters.

After Makishima has been taken into custody, Ginoza is called in by the MWPSB Chief and told that they have lost the authority to investigate Makishima's crimes. Instead, Ginoza's team is tasked with finding the missing Kagari.

After escaping, Kogami visits Saiga to ask for help determining what Makishima's next move will be. Although Division 1 is assigned to capture Makishima alive and execute Kogami, Ginoza still hopes he can get Kogami to surrender before he kills Makishima.

Following Makishima and Kogami, the CID Division 1 detectives arrive at the facility where the Uka-no-Mitama virus is managed. Now it's a race between Kogami and the CID to see who can get to Makishima first and stop him from releasing the modified virus.