"Parasites" are tennis ball sized creatures, whose numbers and origins are unknown. They invade and take over the human mind in order to survive. Shinichi Izumi is a 16-year-old high school student who lives with his parents in a quiet neighborhood. One night, a Parasite invades Shinichi's body in an attempt to take control of it. However, it fails to complete the takeover process and ultimately ends up inhabiting only his right arm.

Thus, both Shinichi and the Parasite—who calls himself Migi—retain their individual minds. Now in a peculiar "human and alien" relationship, Migi proposes that they cooperate to survive. Shinichi has no choice but to agree, and he must now cling to his morality as he and Migi face off against other bloodthirsty Parasites.