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.

Keiichi and Rena suspect that Mion might be related to Rika and Satoko's disappearance, and confront her at her house. There, he learns from her about the burden she carries as the heir of the Sonozaki family, and tries to dissuade her to surrender herself without success.

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.

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

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.

Influenced by Keiichi's encouragement, and the fact her friends are starting to avoid doing the same mistakes again by remembering glimpses of what they could have done, Rika decides to find a way to prevent her ominous destiny by herself.

Hanyū watches silently and hopelessly as the cruel events occur during the dam incident, while she and Rika eagerly await the arrival of the one person who will be the key element to bring an end to the enemy's intentions.

More details about Satoshi's past are revealed, including the reason for his disappearance. Rika and Hanyū make their final preparations for the impending struggle against destiny.

False information regarding Rika is spread by Oishi's group at the precinct, leaving the villain's crew in disarray, and racing against time to prevent their plans from being foiled.

Finding that Tomitake is captured, Irie rushes to escape and ends up meeting with Shion and her bodyguard, Kasai, on their way to the Sonozaki Estate. However, by accepting their help, he ends up unintentionally revealing Rika's hideout to the enemy.

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.