One year after the events of Matsuribayashi-hen, the club has changed significantly; Mion Sonozaki has graduated and moved to Okinomiya while Keiichi Maebara has taken over her duties as class representative and club president. More of their classmates have joined the club and participate in the club's after-school activities. Rika Furude, freed from her cyclical torment, decides to study for the entrance exams to St. Lucia Academy and asks Satoko Houjou to join her. Though initially reluctant, Satoko agrees and the pair spend the next year and a half studying rigorously. In 1987, the pair are admitted into St. Lucia Academy. They are placed in separate dorms and their social lives begin to diverge; Rika joins a group of high-society students and impresses them with her debate skills while Satoko avoids making new friends. Satoko's grades begin to falter and she is made to join a remedial study hall in order to continue attending the Academy. Some time later, the pair return to Hinamizawa to meet their old friends. While there, Satoko wanders into the Saiguden and finds a broken horn. Upon touching the horn, Satoko is greeted by a mysterious being.
The being brings Satoko to the Sea of Fragments and grants her the power to travel between fragments just as Rika is able to do. Satoko travels back to 1983 and initially attempts to prevent Rika from going to St. Lucia Academy at all but finds she is unable to successfully discourage her from doing so. The pair end up studying for the entrance exams just as before and similar events play out, with Rika becoming socially and academically successful while Satoko struggles. Satoko brands Rika a traitor and vows to prevent Rika from ever leaving Hinamizawa. She asks the mysterious being to allow her to view every fragment Rika experienced. After doing so, the being grants Satoko the ability to travel fragments alongside the same iteration of Rika as long as the two die at similar times. The being also asks Satoko to name her; Satoko mumbles in confusion and the being accepts this as the name "Eua". Satoko goes through countless loops to learn more information and formulate a plan to torture Rika. After some time doing this, Eua warns Satoko that her excessive looping is causing fragments to bleed into each other; some character begin to "remember" events from other fragments. Notably, Satoko's abusive uncle, Teppei Houjou, begins having nightmares of his death in one fragment. In this fragment, Teppei reforms and attempts to mend his relationship with Satoko. Seeing this unsettles Satoko but she decides she can find a way to use these "memories" to her advantage. Satoko finds a fragment wherein Miyo Takano "remembers" her failure to execute the Great Hinamizawa Disaster and breaks into a room in the Irie Clinic to steal a syringe full of H-173. Using this, Satoko is able to cause the tragedy of Hinamizawa Syndrome in whomever she wants, whenever she wants.