Mysterious aliens called “Parasites” suddenly begin their invasion when some of them infect humans by entering their brain. One of them attempts to enter the brain of high school student Shinichi Izumi, but resorts to infecting his right hand after failing to bypass his headphones. Thanks to this way of entry, Shinichi retains his human consciousness, unlike the other victims. After his initial shock, Shinichi befriends the parasite and names him “Migi” (Japanese for “right”).
The parasites terrorize humanity by secretly killing them as sources of food. Shinichi himself has to fend against the parasites who are disgusted of the fact that his body exhibits two consciousnesses. One of the parasites also possesses Shinichi’s teacher, Ryoko Tamiya; however, Tamiya is a lot more reasonable and is interested in studying the humans’ way of life, which she does by becoming impregnated with fellow parasite Mr. A. Tamiya explains that despite having parasite parents, the baby she carries is a normal human.
When Mr. A’s attack on Shinichi fails and results in his vessel’s destruction, he transfers his consciousness to Shinichi’s mother, Nobuko. Nobuko returns home and mortally injures Shinichi, although Migi manages to save him by using his essence to renew his heart, essentially infecting Shinichi’s entire body with Migi’s particles. Since then, Shinichi’s personality starts to merge with that of Migi, namely, being apathetic to emotions; this results in Shinichi’s estrangement from his girlfriend, Satomi Murano.
Meanwhile, an underling of Tamiya, Takeshi Hirokawa, runs for mayorship in order to set up the town for the parasites’ interests. Another parasite, Hideo Shimada transfers to Shinichi’s school and initially acts friendly, but when a student discovers his true identity, he massacres the students. Shinichi is able to kill Shimada, who is left to his fate by Tamiya due to a disfigurement that Satomi causes, which makes him unable to control himself. Tamiya gives Shinichi the location of the Mr. A-possessed Nobuko before leaving the scene. At their meeting, Nobuko is able to overcome her parasite’s consciousness long enough for Shinichi to safely kill her.
The epilogue details Hirokawa’s successful run for mayorship, the appearance of the mysterious parasite Goto, as well as Shinichi’s visit to Satomi at the hospital, where an unknown individual records him talking with Migi.
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