Because his father is working abroad, Kōichi Sakakibara moves to his birth town of Yomiyama to live with his grandparents and his aunt Reiko Mikami, where he spends the first month hospitalized due to a pneumothorax. His classmates, Izumi Akazawa, Tomohiko Kazami and Yukari Sakuragi, visit him but act strange. In the hospital, Kōichi meets an uncanny girl, Mei Misaki. Once he recovers, he attends school, where Mei says that their class, Class 3-3, is close to death.

At school, Kōichi's classmate Naoya Teshigawara lets slip that Class 3-3 is cursed. Troubled by Mei but drawn to her, Kōichi asks Sanae Mizuno, a nurse at the hospital, about a girl who may have died on the night of his discharge. Sanae reveals that a student did indeed die that night, and her name might have been Misaki, shocking Kōichi. He enters a mysterious doll shop, where he finds a doll with Mei's likeness, and meets Mei herself, who decides to show Kōichi what is under her eye-patch.

Mei reveals that one of her eyes is a doll's eye that can see strange things. She tells Kōichi the haunted legend of the town: a student from Class 9-3 of 1972 also named Misaki died but the class continued acting like Misaki was alive, thus inviting death. Kōichi's classmates avoid the story whenever he asks them about it. He learns that the girl who died in the hospital was Misaki Fujioka, Mei's cousin. After Mei claims that she can only be seen by Kōichi, Yukari starts to flee from them. However, she slips on the stairs that lead up to Class 9-3, impaling her neck on her own umbrella. Later that day, Yukari's mother also dies for the same reason.

Kōichi encounters classmate Aya, whom he manages to save when they are nearly hit by a falling sheet of glass. At the doll shop, Mei tells Kōichi that "it has already begun". Kōichi confronts his classmates about not telling him what is going on. Sanae then contacts him, saying that when she asked her brother about Mei, he panicked and insisted no such person exists. Sanae then enters the elevator, which falls down the shaft and kills her. Kōichi hears the crash over his cellphone.

Ikuo Takabayashi dies next from a fatal heart attack, and Kōichi's classmates start ignoring him. Mei explains that she does exist. After the 1972 Class 9-3 incident, there was always an extra student in the class. The "extra" was dead but did not know it. No one could identify who it was, and the deaths began, year after year, with no one remembering the "extra" after graduation; they would disappear. To prevent this, the class treats one student like they do not exist to make up for the student who is actually dead. This year, it is Mei, and now Kōichi.

Shōji Kubodera, homeroom teacher of Class 9-3, commits suicide in front of the class. The class realizes that the "charm" has not stopped the curse, and begin acknowledging Kōichi and Mei again. Kōichi learns about Katsumi Matsunaga, a former Class 9-3 student who managed to stop the phenomenon in 1983, leaving a clue on how he did it for future students to find. Kōichi fears he may be the "extra" dead student this year, but Mei tells him he is not.

Kōichi, Izumi, Naoya and Yūya, along with classmates Takako Sugiura and Junta Nakao, go to a beach resort to meet Katsumi. They relax when they leave Yomiyama, convinced the curse is ineffective outside town. At the beach, Kōichi discovers Mei, and the group enjoys a fun afternoon. Katsumi joins them, but the only thing he remembers is that he left the clue in the classroom. When Junta drowns and his body is torn up by a motorboat, everyone realizes that the curse may not be limited in Yomiyama.

Chibiki reveals that Junta's death stemmed from a head trauma he received while still in Yomiyama. Kōichi finds Katsumi's clue: a cassette tape, in which Katsumi explains what happened on the school trip to the Yomiyama Shrine fifteen years ago. Two students died, but something very important happened. Before it can be revealed, Naoya accidentally breaks the tape but Yūya offers to repair it. Aya and her family were later killed in a road accident while escaping town as a boulder forces their vehicle into a ravine, and Yumi Ogura's brother dies after a runaway truck carrying an excavator smashes into his apartment.

Class 9-3 goes on a trip to the Yomiyama Shrine, where the group listens to the repaired tape. Katsumi had accidentally killed one of the students, and when he discovered no one remembered the student, he realized he had killed the "extra", and thus stopped the curse. Mei reveals that her cousin Fujioka was actually her twin sister, meaning that her death was the first of this year's curse. Mei also says that her doll's eye sees the "color of death", her proof that Kōichi is not the "extra".

Kōichi finds that the manager has been killed, the dining hall is on fire, and the tape has gone missing. Naoya and Yūya are attacked by the hotel mistress, who has gone insane. Takako believes Mei is the "extra one", noticing a difference from the Misaki she knew in elementary, probably Fujioka. Takako, ensuing chaos, broadcasts the tape to the class, prompting everyone to kill Mei. Two students die while trying to kill Mei and one dies by a sudden backdraft.

Tomohiko is randomly killing students to find the "extra" but is killed by Izumi, who is soon killed by glass shards impaling her, after which she remembers briefly meeting Kōichi in Yomiyama in 1996. Kōichi learns that the "extra" is Reiko, who was actually murdered in 1996. His memories, altered because of the curse, return to him and he remembers he had come to Yomiyama in 1996 for Reiko's funeral. He reluctantly kills her, ending the calamity, but passes out from the shock. Later, Kōichi and Mei reflect on the memories they will soon forget. After the credits, Naoya records a new message for those who may face the calamity in the future.