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.
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.
Shinichi starts his battle with Miki. After some quick thinking, they use their environment and their observations to launch a successful counter attack. Little do they know, Miki is not the alpha Parasyte in that body. In fact the Juggernaut I’d been waiting for was inside of him all along. Driven to his limits, Shinichi goes into hiding.
Shinichi starts to track Parasytes, eventually finding one of their feeding grounds. After successfully defeating another Parasyte, he starts to feel overconfident about his abilities. The Parasyte Council, finally sick of his interloping, sends a team of Parasytes after him. Intelligent and sociable, this group is a dangerous threat. However, what is most frightening is they all inhabit the same body.