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...
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...
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...
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 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!
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...
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...
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...
As Shinichi and his parasyte continue their unasked-for coexistence, the parasyte in his right (migi) arm decides to take on the name of "Migi." Shinichi realizes that parasytes are involved in the ongoing mincemeat murders. Feeling alone in his discovery, Shinichi grapples with frustration. Unbeknownst to him, he is about to meet another parasyte for the first time...