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.

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!

Though still full of doubt, Kuramori has, for the time being, accepted Shinichi. Soon after, Kuramori's resolve is severely shaken by witnessing a parasite murder a human being. Shinichi is frustrated by the turn of events, but the lull is cut short when a new parasite appears...

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...