After moving into the quiet town of Hinamizawa, Maebara Keiichi spends his days blissfully in school often playing games with his local friends. However, appearances can be deceiving. One fateful day, Keiichi stumbles upon news of a murder that had occurred in Hinamizawa. From this point on, horrific events unfold in front of Keiichi, as he soon learns his close friends may not be all that they seem. Based on the amateur mystery game by 07th Expansion, the story is told in a series of different scenarios.
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.
Back in June 1983, the club participates in a game of "zombie tag". On their way home, they run into Irie, Tomitake, and Takano, who tell Keiichi about the yearly murders known as "Oyashiro-sama's Curse". However, he understands why his friends hid it from him and doesn't resent them for it. Regardless, this fails to reassure Rika, as she grows progressively depressed as the day of the Watanagashi Festival approaches.
Satoko worries about Rika's depression and tries to confront her about it, but Rika continues to deny anything is wrong. In the middle of the night, Satoko is woken by Rika arguing with a mysterious voice, and telling her she will soon be murdered, and there is nothing that either of them can do.
The day of the Watanagashi Festival comes, and once again Rika fails to warn Tomitake of his imminent death. Later, Satoko is convinced that a mysterious man is following her and Rika around, even though no one else has noticed any such thing. Worried of Rika's safety, she sets traps around the house to alert her of any intruders, and when one is triggered, her fears are confirmed.
Much to Satoko's surprise, Rika hides her before letting her murderers take her away. After witnessing Rika's demise and the death of the remaining villagers, Satoko fights desperately for her life.
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.
The fight to save Satoko from her uncle's abuse continues, but they stumble on a dead end because she is reluctant to denounce him, for her own reasons. Rika realizes that despite their, she is the one who must take action.
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.
After getting a clue of the villain's betrayal, Rika tells her friends the truth behind the Hinamizawa Syndrome, and her connection with it. Meanwhile, the enemy moves on with their plan, eliminating any opposition.
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.
Takano's past is revealed in disjointed flashbacks, some of them showing her harsh childhood, while others to the time when she became involved with researchers of the Hinamizawa Syndrome.
Takano's story continues, including how she met her foster grandfather, and her determination to continue his work. A few years later, Takano and Hanyū have a very heated confrontation at Oyashiro-sama's shrine.
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.
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.
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.
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.
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.
Irie, Kasai, and Shion head to the clinic to rescue Tomitake. Irie finally unveils to Shion where Satoshi disappeared to and the others deal with the enemy assaulting the mountains on their location
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.