Keiichi Maebara, a student who recently moved into the village of Hinamizawa, is invited by his new friends at school to join their club. But while searching for treasure at a garbage dump with Rena Ryugu, he discovers the village is not as peaceful as it seems.

Delving further into the mysteries surrounding the village, Keiichi's paranoia grows after he starts to suspect that someone might be after his life.

Akasaka and Oishi find the kidnappers' hideout and rescue the boy. After discovering that their efforts were in vain because the perpetrators' demand was already conceded, he realizes the real meaning behind Rika's words to him.

Keiichi tries to dissuade Rena, but is confronted by her with his own dark secrets. After confessing his past sin to his friends, he finds that he can recall events from Onikakushi-hen, even though they have no bearing on the current situation.

Rena's madness reaches the peak to the point of taking all the school children hostage. With the police's help and working together with the rest of the group, Keiichi manages to defuse a homemade bomb Rena planted on the rooftop of the school. There, the two have a final confrontation and even though he is defeated, Keiichi manages to get Rena to realize she should have trusted and confided in her friends.

Back in June 1983, the club participates in a game of "zombie tag". On their way home, they run into Irie, Tomitake, and Takano, who tell Keiichi about the yearly murders known as "Oyashiro-sama's Curse". However, he understands why his friends hid it from him and doesn't resent them for it. Regardless, this fails to reassure Rika, as she grows progressively depressed as the day of the Watanagashi Festival approaches.

At last, Rika persuades Satoko to ask for help and she is freed from Teppei. However, just when the village seemed to be relieved from its eternal cycle of hatred and death, the real enemies start to act, just like they did in previous worlds.

The rest of the Yamainu concede defeat, but Takano is unwilling to surrender. After learning Nomura in Tokyo planned to use her as a scapegoat, she flees into the mountains and has a final confrontation with Rika's group. In the end, the Banken comes to arrest her, but Tomitake, pitying her and seeing how she had been infected with the Hinamizawa Syndrome, takes her into the the Irie Clinic for treatment. At the end, Rika and her friends Hanyū, Keiichi, Rena, Satoko, Mion, and Shion, attend the festival.