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!

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.

The assault squad succeeds in eliminating Hirokawa, the parasites' leader, but they find themselves in a bind when the ultimate parasite appears. Their failure to eliminate Gotou strikes fear into Shinichi's heart--who will give him the final courage to face Gotou?

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...