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.
Realizing that he forgot to pack his bathing suit while rushing to meet his friends at the pool, Keiichi borrows a pair of trunks from Mion's uncle, who claims that these trunks have the magical ability to make women attracted to whoever writes their name on them and wears them for three hours. Later, Mion hears from her uncle that he had made a mistake in describing the abilities of the trunks, revealing that the person whose name is written on the briefs will fall in love with the wearer, meaning Keiichi, who had written his own name on them, will fall in love with himself. Not wanting Keiichi to become a narcissistic jerk, the girls try to talk him out of taking the trunks off, though Keiichi thinks it's a trick so they can force him to wear an embarrassing pair of trunks they provided. Knowing Keiichi won't go down without a fight, the girls rally everyone at the pool to chase him down and retrieve the trunks by force, even going as far as turning Keiichi's only supporters (Tomitake, Oishi, and Irie) against each other and fight over wearing the trunks for themselves. Finally, the trunks are removed before time runs out, though the naked Keiichi still refuses to wear the girls' embarrassing trunks.
Now that she and her friends are finally free from the eternally repeating tragedies of June 1983, Rika has a new lease on life. While biking with her friends, Rika carelessly collides with an oncoming truck and is apparently killed; when she awakens, she finds herself in another Hinamizawa. However, this world is quite different from other worlds in the past: Keiichi, Takano, Irie, and Hanyuu are nowhere to be found; she is no longer close friends with anybody, Satoko being particularly hostile; the dam project that threatens to flood the town is still underway; and none of the successive tragedies she witnessed countless times happened at all, meaning Satoshi and her own parents are still around. For the first time in her life, Rika is at a complete loss for what to do.
Rika finally makes contact with Hanyuu, who tells her that for her to return to her old world, she must find and dispose of a piece from her old world that prevents Hanyuu from entering this new world, which in turn prevents Rika from reincarnating—if this piece turns out to be a person, for instance, she must kill that person. She is initially eager to find the item and return to her old world, especially when she responds to Satoko's bullying by assaulting her. Shortly afterward, however, Rika experiences what life with a mother is like, and begins building a new friendship with Mion, Rena, and Satoshi, as well as making peace with Satoko. Rika now feels it's all a matter of deciding which world she would rather like to stay in until she learns that her mother, now the reincarnation of Oyashiro instead of Rika, is the item she must dispose of.
Rika becomes gradually more torn between remaining in this new world that knows no sin where everyone is living contently, or killing her mother and returning to her old world, and is devestated to learn that she does not have much time to act. Finally, Rika decides to fight for what she wants to live for. The next thing she knows, she awakens from a coma in her old world and happily reunites with her friends, the other world having apparently been a dream, though Rika concludes she must have killed her mother to regain consciousness nonetheless. Unbeknownst to her, however, the dream was developed by Hanyuu to teach Rika, as her friends help her realize, that people need to work past personal hardships in order to make life worth living.
During a picnic with Keiichi, Rena accidentally swallows one of the mysterious "Fuwazaru Magatama" which falls from the sky, and begins acting lovesick. Rika explains that the seal on the magatama has been broken, and that whoever possesses the red magatama will fall blindly in love with anyone holding its white counterpart. Everyone reasons that Rena must have swallowed the red magatama and sets out to stop her and find the white magatama, though it winds up in the possession of Tomitake, then Takano, and finally Oishi, each of whom gradually come to accept her love under the magatama's curse and refuse to relinquish it. Keiichi finally manages to obtain the magatama after beating Rena and Oishi with Akasaka in a game of mahjong; unfortunately, Oishi fumbles it and Keiichi ends up accidentally swallowing it as well. Fortunately, Rika lifts the curse before Keiichi can fall under its power, which returns Rena to normal. In the process, Rena, who is grateful to Keiichi for helping her, expresses her feelings toward him, though she isn't sure if it's part of the magatama's power. Unfortunately for Rena, Tomitake and Takano still appear to be infatuated with Rena and fight over who gets to keep her.