On Christmas Eve, Hiro Hirono runs into Miyako Miyamura, a frivolous girl who borrows his bicycle in order to chase down a purse thief. After Hiro finds his bicycle wrecked and Miyako unconscious, the two unexpectedly spend their Christmas Eve together, and when they discover they go to the same high school, their accidental relationship develops even further. This sparks the jealousy of Hiro's childhood friend Kei Shindou, whose pure approach to life catches the eye of Kyosuke Tsutsumi, a womanizing photographer searching for the perfect shot. Elsewhere, Renji Asou, a boy who dreams of being a girl's knight in shining armor, has a chance encounter with Kei's twin sister—the overly shy Chihiro Shindou, who spends her time reading alone—at an abandoned train station. The two quickly become friends and eventually decide to write a novel together. However, when Renji discovers Chihiro's secret, his childish ideals are put to the test. Guided by two mysterious adults, these youths' relationships intertwine in a heart-rending tale of love, rejection, acceptance, and memories.

The infamous series of unexplainable murders in Hinamizawa have been solved and the chains of fate have broken due to the efforts of Rika Furude and her friends. Rika believes she has finally obtained the normal and peaceful life she desired with her friends; however, she is proven wrong when the wheels of fate begin turning once again after an unfortunate accident. Rika suddenly finds herself in a perfect world, the constant cycle of brutal killings having never taken place, where all of her friends are content and satisfied. Not wanting to abandon the world that she fought so hard for, she learns she must destroy an essential key to get back. But can Rika abandon the faultless world she is given the chance to live in, after all of her battles have brought her this far?

While at school, Mai Taniyama and her friends like to exchange ghost stories. Apparently, there is an abandoned school building on their campus that is the center of many ghost stories. During the story, they are interrupted by a mysterious male figure. The person turns out to be Kazuya Shibuya, a 17-year-old who is president of the Shibuya Psychic Research Company. He was called by the principal to investigate the stories surrounding the abandoned school building. The next day, on the way to school, Mai passes the school building in question. While examining a strange camera she spotted inside, she gets surprised by Kazuya's assistant. Unknowingly interfering with the investigation, Mai breaks the camera and Kazuya's assistant gets injured. Kazuya forcefully hires Mai in order to pay for the camera and replace his injured assistant. From that point on, Mai begins to learn about the paranormal world and the profession of ghost hunting.

Rika Furude and her group of friends live in the small mountain village of Hinamizawa; in June 1983, they welcome transfer student Keiichi Maebara into their ranks, making him the only boy in their group. After school, they have fun playing games and spending each day living their lives to the fullest. Despite this seemingly normal routine, Keiichi begins noticing strange behavior from his friends, who seem to be hiding the town's dark secrets from him. Elsewhere, a certain person watches these increasingly unsettling events unfold and remembers all the times that this, and other similar stories, have played out. Using that knowledge, this person decides to fix these broken worlds. However, when certain variables change, the individual is faced with a horrifying realization: they have no idea what to expect or how to stop the impending tragedy.