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.

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.

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.

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.

Shion believes the Sonozaki family is connected to the acts of "demoning away" people in the village, especially that of Satoshi. She imprisons Mion in the dungeon and unintentionally kills her grandmother. Shion pretends to be Mion the next day and confronts Keiichi about the previous night's encounters, to which Keiichi still denies. Later, she finally discovers the ones responsible for Satoshi's disappearance.

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.

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.

Rena disposes of Rina and her lover Teppei, after discovering their plan to con her father. Discovered by her friends, she ends up getting support by them, and they help her hide the bodies, but during the night of the Watanagashi festival, she is interrogated by Oishi and wonders if he suspects of her.

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.

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 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 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 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.

Satoshi apologizes to Shion (still pretending to be Mion), and asks her to care for Satoko during the Watanagashi Festival. That night, his aunt is murdered; in order to cover for Satoshi, Shion reveals that she is actually Mion's twin sister. After the police questions her, she is brought back to the Sonozaki main estate to answer to her grandmother for all the trouble she has caused.

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.