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 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.

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.