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.

Keiichi's mentality is shaken when his friends tells him that he was actually at the Watanagashi Festival with them and Satoko still bemoans her uncle's abuse, despite being sure about having him dead. His confusion grows when he tries to unsuccessfully find the truth.

Four years ago, during the dam incident, young police investigator Mamoru Akasaka comes to Hinamizawa to find leads to a child kidnapping. After hearing an enigmatic warning from a younger Rika, Mamoru becomes suspicious of some of the townsfolk.

The events from Watanagashi-hen are retold from another point of view. Shion takes Mion's place in Hinamizawa and is lovestruck by Satoko's older brother, Satoshi, at their first meeting together. But after discovering about the trouble he spends to protect Satoko, Shion starts to loathe her.

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.

Shion has captured the village head and gets information about the town involving the previous murders and Satoshi. Later, Shion confronts Rika about the murders, leading to a confrontation between the two. Once night falls, the truth behind Rika and Satoko's disappearance at that night is revealed.

Rena discover the true character of her father's girlfriend and grows a deep hatred for her.

While studying Takano's scrapbooks, Rena starts to unveil the the truth behind Oyashiro-sama and Hinamizawa's dark past.

Hanyū is physically introduced into the world as a transfer student to the Hinamizawa school, but forgets her role. After a brief meeting with Takano and Tomitake, she remembers the past worlds and informs Rika about the enemy's intentions.