The whole world is about to change one quiet evening with the arrival of parasytes who devour human brains. One of their eggs lands at the home of Izumi Shinichi, a high school student. The hatched parasyte attacks Shinichi, but it faces unexpected resistance and fails to infiltrate his brain.

Struck through the heart by his mother-turned-parasite, Shinichi survives only through Migi's efforts. After regaining consciousness, Shinichi is devastated by the realization that none of it had been a dream.

Shinichi has regained some semblance of a normal life. However, with Migi's cells dispersed throughout his body, his physical abilities have greatly increased to the point that not even Mitsuo poses a threat. Shinichi fears that the changes go beyond the physical and into the psychological. Just as peace returns to his school, a new parasite appears!

Yuko is drawn to Shimada Hideo, but gradually realizes that something is seriously amiss with Shimada's face itself. As Yuko pursues Shimada's secret, she connects the dots between him and her brother's police investigation.

Kana's feelings for Shinichi grows day by day, and so does Shinichi's apprehension about Kana's ability. As ordinary life returns, Satomi struggles with her mounting suspicion that something has changed in Shinichi. Meanwhile, a new parasite appears to wreak havoc in a local gang hideout. Everyone's lives are about to get shattered yet again.

Shinichi's secret becomes known to Kuramori, the private investigator hired by Tamura. Shinichi tries to confide in Satomi, but his unsuccessful attempt only drives a wedge between them. Shinichi recruits Uda's help to break the impasse.

Shinichi and Migi arrive at the park, only to find Tamura holding her child. As Shinichi struggles to quell his fury at the sight of her, Tamura unleashes a flurry of questions about the meaning of the parasites' existence and what humanity means to them.

Motivated by Satomi to stay alive, Shinichi resolves to fight Gotou. With Migi's support, they press their attack in an isolated forest. However, they fail to finish Gotou at a critical juncture, causing Shinichi to lose Migi and flee in defeat.

With Gotou's defeat, Shinichi's life is finally back to "normal." Though saddened by Migi's sudden departure, Shinichi moves forward with his life. However, a final threat appears...