Saori Mugino, a devoted single mother, finds herself deeply concerned about her fifth-grade son, Minato, who has started displaying peculiar behaviors. These troubling signs include cutting his own hair and returning home wearing only one shoe. The situation escalates when, one fateful night, Minato fails to come home at all. After several frantic phone calls, Saori ultimately discovers her son in an abandoned train tunnel. This incident prompts her to suspect that Minato’s teacher, Mr. Hori, may be mistreating him, leading her to confront the school administration. Unfortunately, she is met with an unempathetic response from the faculty, culminating in a hollow apology from Mr. Hori.
Upon confronting Hori directly, Saori is shocked when he insinuates that her son might actually be bullying another student, Yori. Determined to uncover the truth, Saori pays a visit to Yori’s home. Despite Yori's own odd conduct, he expresses a genuine concern for Minato, hinting at a deeper connection between the boys. Eventually, Mr. Hori is dismissed from his position, but not before Minato suffers a terrifying fall down a flight of stairs while trying to avoid him.
A stormy night becomes a pivotal moment when Hori unexpectedly arrives at Saori and Minato’s home, only for Saori to find that Minato has mysteriously disappeared. The narrative then transports viewers back to the beginning, exploring events from Hori's perspective. Here, it's revealed that he had previously observed Minato engaging in disruptive activities, including throwing classmates' belongings and being involved in a troubling incident with Yori.
As Saori pursues answers regarding Minato's welfare, she faces immense pressure from the school staff to remain silent in order to safeguard their reputation. Ultimately, the pressure mounts on Hori, leading him to resign after being attacked by the media and abandoned by his girlfriend. One fateful day, curiosity drives Hori to visit Yori's house, where he encounters Yori’s father, Kiyotaka, who is struggling with alcoholism and delusions.
The tension escalates until a rainstorm strikes. During this tumultuous time, Hori discovers a typo in Yori's old homework, which seems to spell out Minato's name. This revelation suggests a bond between the boys, prompting Hori to rush to Saori’s home to apologize for his past misunderstandings. Tragically, he learns that Minato has vanished, leading them both to the train tunnel in a desperate search for the boy. They find a dilapidated railcar, nearly swallowed by mud, that holds Minato’s abandoned poncho—a chilling sign of his presence.
In a poignant final flashback, viewers witness the growing friendship between Minato and Yori amidst the backdrop of bullying. Yori faces incessant torment, yet Minato stands up for him, misconstrued by Hori as bullying rather than the protective bond it is. As their friendship deepens, feelings of romantic affection begin to confuse Minato, intensifying his internal struggles about his worthiness in the eyes of his father.
The stormy evening previous to the climax reveals a somber moment where Minato rescues Yori, who is found in a bathtub. They escape to their secret hideout in the railcar, immersing themselves in a world of safety and camaraderie. After the storm passes, the boys emerge with a newfound sense of freedom, proclaiming that they have been reborn, as they run hand in hand through a sunlit field, leaving behind a world filled with pressures and misunderstandings.
