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.

As the number of mincemeat murder victims grows, Shinichi, alone in his knowledge of the truth, is in turmoil. When Migi suddenly alerts him to the presence of another parasyte, he is aghast to find that it is in his own school. Paranoid, Shinichi attends a schoolwide assembly, where the staff introduce a beautiful new teacher...

Shinichi's life returns to "normal" after A's killing spree, but Shinichi remains in low spirits. His mother, Nobuko, becomes worried, but Shinichi just bluffs when she asks him what's wrong. His father, Kazuyuki, suggests to Nobuko that a past incident may be involved. Nobuko looks down at the old scar on her hand and thinks back to what happened when Shinichi was a little boy...

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.

Kana's special ability is gaining in strength. Believing that ignoring her will only endanger her life, Shinichi tells Kana everything about the parasites. Shinichi only wants to save Kana, but Kana believes Shinichi is lying to her. They are two ships, passing in the night...

A few days after Kana's death, things seem to be back to normal for Shinichi. Satomi and her friends are perturbed by his seeming indifference, but Shinichi, himself, is grappling with his own sense of disquiet with his unnatural state of mind. Meanwhile, a man begins snooping around about Shinichi...

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...

The newest parasite to appear is different from the others. Chatty and expressive, the parasite identifies himself as Miki and immediately makes his move. With Migi asleep, all Shinichi can do is to run and keep running...

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.

The joint operation by the police and the strike force to eliminate the group of parasites led by Hirokawa has begun. Yamagishi's unit uses their special sensor system to hunt down the parasites. Amidst the chaos, human victory seems all but confirmed. But the tables are about to be turned by a single parasite...

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...