A summer vacation ends with a tragedy that upends a classroom of boys. Yamada, the beloved center of Class 2-E at Hodaka High School, a private all-boys school, is struck and killed by a drunk driver just before the new term begins. The grief is suffocating. The second term opens in a funereal silence, and the homeroom teacher, Hanaura, attempts to break the pall by suggesting a seat shuffle. No one responds. Then, from the classroom speaker, a familiar voice rings out. It is Yamada. His soul has inexplicably possessed the classroom's speaker system.

The rest of Class 2-E accepts this miracle with surprising speed. Yamada can now only hear and speak, but he is still Yamada. The boys devise a secret code phrase to summon him, and their bizarre and boisterous daily life resumes. The story moves through a series of episodic, comedic arcs: the seat-change arrangement proposed by the now-voiceless Yamada, a raucous birthday competition, and a culture festival class project dubbed "Yamada Cafe." These episodes showcase the quick-witted, profane, and affectionate bonds of the group. Key classmates include Wakutsu, a serious and quietly intense boy who shares a deep history with Yamada from middle school, and other colorful personalities like the investigative duo of Izumi and Kuramochi, who sense a mystery behind the accident.

As the second year ends, the narrative takes a sharp turn. The classmates graduate, enter new lives, and gradually stop visiting the classroom. Yamada ages not at all. He is trapped inside the speaker, forgotten by nearly everyone except Wakutsu. Wakutsu, who was once saved by a single word from Yamada, abandons his own dreams and becomes a substitute teacher at Hodaka solely to stay with his friend. This second half of the story becomes a stark, introspective confrontation. Wakutsu presses Yamada on his death, uncovering a different truth than the simple accident reported at the start. Yamada confesses that he felt profoundly empty, a hollow performer who did and said only what was expected of him, and that in the moment of the accident, he had not cared whether he lived or died. His ghost was a punishment. The climax builds toward a desperate argument in the darkened classroom. Wakutsu destroys the speaker, then the desks, the chairs, and the windows, smashing the physical classroom itself, trying to force Yamada to voice a genuine desire to live. As the classroom is dismantled, Yamada finally screams that he wants to live. The voice stops. The story closes on the silence of the wrecked room, the lingering question of whether that final human cry was enough for Yamada to be freed.