Saori Mugino is a single mother raising her fifth grade son, Minato. He soon begins exhibiting strange behavior such as cutting his own hair and coming home with only one shoe. One night, Minato does not come home at all and after calling around, Saori finds him in an abandoned train tunnel. Saori begins to suspect her son's teacher, Mr. Hori, is abusing him and confronts the school about it. She is treated coldly by the faculty, culminating in Mr. Hori making a disingenuous apology. When she confronts Hori directly, he implies that Minato is actually bullying another student named Yori. Saori visits Yori's house and he, despite his own strange behavior, seems fond of and concerned for Minato. Hori is eventually fired from the school, but returns days later and Minato falls down a flight of stairs trying to escape from him. Hori later comes to Saori and Minato's house during a rain storm, but Saori finds that Minato has gone missing.A flashback returns to the beginning of the film from Hori's point of view. He notices Minato exhibiting disruptive behavior, such as throwing other students' belongings around the classroom and seemingly locking Yori in a bathroom stall. Hori too visits Yori's house, where he discovers that his father, Kiyotaka, is a delusional alcoholic. When Saori begins inquiring about her son, the faculty pressure Hori to let them handle it to protect the reputation of the school, ultimately requiring him to resign. After he is hounded by journalists and left by his girlfriend, Hori returns to the school to confront Minato, and contemplates jumping from the roof of the school after the boy falls down the stairs. During the rainstorm, Hori notices a typo in some of Yori's old homework that seems to spell out Minato's name. Realizing the two boys were actually friends, Hori rushes to the Mugino household to apologize. When Saori tells him Minato is missing, they go to the train tunnel to find him. They find an abandoned railcar nearly buried in mud, but when they open it they only find Minato's abandoned poncho.A final flashback begins from Minato's point of view. Yori is routinely picked on by the other boys for his asocial and seemingly effete behavior. Yori plays with Minato's hair, which the latter then impulsively cuts off. The two boys grow close and Minato begins defending him from other bullies, which Hori confuses for bullying. As the two become closer, Minato is distressed that his feelings are becoming romantic and that he is not a worthy son to his father. One night when he goes to Yori's house, he and Kiyotaka declare that Yori has been "cured," though Yori quickly recants, which incites his father's wrath. During the rainstorm, Minato finds Yori abandoned fully clothed in his bathtub and the two escape to the abandoned railcar, which has become their hideout. After the rain subsides, they emerge from the bottom of the railcar and declare that they have been reborn, and run through a field together.