Things have returned to normal for Shinichi. Changed after his experience with Gotou, Migi retreats into his own mind to ponder his very existence. Living a normal life only lasts so long until the final loose thread comes into play.
Shinichi goes on the offensive against Gotou in a last desperate attempt. Obviously outmatched, he still manages to survive much longer than Gotou anticipated. After remembering the municipal building incident and getting a lucky strike in, the tide begins to change.
Shinichi barely gets to enjoy his afterglow before being put on the run by Gotou. Using their heads and resorting to extreme measures, they still fail to bring him down. Battered and beaten, Shinichi escapes to a rural village. While Gotou continues to search, the livelihood of the villagers is put at risk.
Hirokawa reveals his reasons for creating his Parasyte haven, and his final secret is revealed. Meanwhile, Gotou is still on the rampage, and eventually finds his way to Shinichi. Weakened from taking down the many exterminator squads, he decides to retreat, but not before giving Shinichi a clear threat. Starting to struggle with paranoia, Shinchi finds consolation in the arms of Murano.
The police try to keep things in order, but human error makes the situation quickly devolve into martial law. On the hunt for Parasytes, the protection of civilians is a secondary concern. Two groups find Gotou, and his invincibility is once again put to the test.
Shinichi confronts the killer in front of him. His loss of cool makes Hirama even more suspicious. While Shinichi tries to go back to a peaceful life, Hirama ropes him in for the final assault on Parasyte headquarters.
Tamura uses her final moments to give Shinichi a message about what her Parasyte experience has meant to her. In the wake of her death, Shinichi finally comes to terms with the loss he has experienced. Now under police protection, Shinichi continues to give no hints to his true nature. Still suspicious, the police use their last ace in the hole.