العالم بأسره على وشك التغيّر من عالم هادئ إلى صخب مع وصول الطفيليات الذين يلتهموا المخ البشري. أحد البيضات الخاصة بهم تسقط على منزل إيزومي شينتشي، طالب في المدرسة الثانوية. الطفيلي الذي تفقّس هاجم شينتشي، لكنه واجه مقاومة غير طبيعية وفشل في التسلل إلى مخّه.

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...

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...

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...

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.

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...

Having determined Tamura to be a threat, Kusano's group moves to eliminate her. Meanwhile, Kuramori moves to avenge his family's death by abducting Tamura's baby. With her baby in his arms, Kuramori faces Tamura and threatens to throw the infant down a steep slope--what will Tamura do?

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...

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...

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?

Motivated by Satomi to stay alive, Shinichi resolves to fight Gotou. With Migi's support, they press their attack in an isolated forest. However, they fail to finish Gotou at a critical juncture, causing Shinichi to lose Migi and flee in defeat.

With no chance to survive, Shinichi pulls off a desperate move.

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...