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.

The annual Watanagashi Festival finally starts, and everyone has fun feasting and playing games. However, in the following day, Keiichi is interrogated by chief police officer, Oishi, about a crime that occurred at the night of the festival, and he starts fearing the villagers might be involved in this and other similar incidents, like Oishi suspects.

During Rika's ritual performance at the Watanagashi Festival, Shion whisks Keiichi away to sneak into the forbidden shrine warehouse, where Tomitake and his friend, Miyo Takano, are waiting. However, after learning about the other pair's fate, he starts to worry about his and Shion's safety.

Satoko is absent from school for a few days. After discovering that the cause of her absence is Teppei, her abusive uncle, who left Hinamizawa after his wife was murdered on the night of Watanagishi, but recently has returned, Keiichi decides to intervene.

Upon talking with Ōishi, Shion finds out Satoshi has gone missing and decides to investigate further into the mysterious murders over the past four years. One day at the library, Shion meets Takano, who tells her more on the history of Hinamizawa and its dark past. As the story skips one year to the present day, similarities between Keiichi and Satoshi brings back memories of Satoshi to Shion.