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...

Running late to school, Shinichi sees Nagai in trouble with some punks. When Shinichi steps in to help, he meets a high school student, Kimishima Kana. Shinichi and Satomi share a close moment when she tends to his injuries, but his life is about to take a sudden turn with a single phone call from his father...

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.

Thinking he'd found his mother's killer, Shinichi instead meets Uda Mamoru, a man in a similar situation as himself. Uda sympathizes with Shinichi and suggests that they all work together. The time to avenge his mother has come at last! Shinichi heads to the precipice...

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.

Incapable of rationala thought, Shimada Hideo is a savage beast on a rampage, and Satomi's class has become his prey. Shinichi must make his way through the carnage in order to save Satomi...

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...

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.

Suspecting Shinichi's connection to the parasite cases, Hirama arranges to have Shinichi meet with Uragami, a convict with a peculiar ability. Although cleared of any suspicion and able to return to his high school life, it isn't long before Hirama appears once more before Shinichi. A government operation to neutralize the parasites with Hirokawa is about to begin...