Keiichi's struggle to help Satoko forces him to confront the village elders, even the leader of the Sonozaki family. As the government succumbs to the pressure of Keiichi and his allies', Satoko's condition is also at its limit.

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.

One after another, Rika's friends are killed while trying to protect her. Takano dissects Rika, but does so without anesthesia, as requested by the latter in an attempt to carve the identity of the culprit behind all the Hinamizawa murders in her mind and prevent the events from this and past worlds from repeating themselves. The villagers are rounded up at the school and gassed to death, while an ecstatic Takano proclaims her ascension to godhood.

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.

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.

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

Keiichi's despair reaches its peak. After being captured and sedated, he wakes up restrained by Mion and Rena, and they attempt to inject him with a mysterious drug. Keiichi murders them before taking his own life by clawing his throat.

Mamoru Akasaka, with an assistant, visits the abandoned town of Hinamizawa in the year 2007, and meets with Officer Oishi. They still wonder about the Great Hinamizawa Disaster that decimated the town and the connection to Miyo Takano's File No. 34. Rena shares with them the little knowledge she has about Rika's strange behavior, shortly before the supposed "gas leak", and Akasaka recalls his meeting with the young Rika as well.

Rika begins a new world with Hanyū, but is getting tired of seeing her friends commit the same acts that lead them to terrible mistakes, until Keiichi proves to her that people can change their destinies if they want.

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.

Rika's plans are hindered by the appearance of Teppei, who much like in "Tatarigoroshi-hen", begins to abuse Satoko. Keiichi and the rest of the gang decide to find a way to release her from his clutches, but the government is reluctant to cooperate.

In order to save Satoko, who is terminally infected with the Hinamizawa Syndrome, Rika offers herself as a test subject for Irie and Takano's research. More light is shed into the deaths of Satoko and Rika's parents, and its involvement with the legend of Oyashiro-sama's curse.

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.

Rika gather her allies and start to make plans, while obtaining more information about the enemy and those supporting their ambitions.

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.

Shion tricks Keiichi in a phone call and later tricks the townsfolk in order to make Keiichi a murder suspect, however she quickly realizes that Oishi suspects her instead. When discovered by Rena and Keiichi, Shion lures Keiichi away and knocks him out in front of Mion. The truth behind the sisters' fate is revealed.

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.

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.

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 parents leave for Tokyo for a few days. Helped by Satoko and Rika, who makes dinner for him, Keiichi learns about Satoshi, Satoko's older brother, and his mysterious disappearance on the night of last year's Watanagashi.

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 comes to the resolution that he must kill Teppei. After brutally beating him to death with Satoshi's baseball bat, he buries the body, and on his way back home, Keiichi bumps into a suspiciously acting Takano.

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.

Keiichi goes over to the Houjou residence to ascertain Teppei's existence and finds Satoko in need of clinical help. At the Furude Shrine, Keiichi discovers Rika's disemboweled body, and Satoko believes that Keiichi is the culprit and flees. After fruitlessly trying to convince her that he is not the murderer, disaster strikes the town of Hinamizawa.

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.