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 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...

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...

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?