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.

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.

Keiichi meets Mion's twin sister, Shion; the two are so identical that Keiichi can hardly tell the difference between them. It is also revealed that Mion has a crush on him.

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 asks Rika for help, but when she and Satoko disappear, he starts fearing for the worse.

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.

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.

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.

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.

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.

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 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.

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

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.

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.

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.