In occupied France during World War II, a precocious and intelligent young boy named Julien Quentin bids farewell to his mother at a train station before returning to his Catholic boarding school. The austere institution is run by a group of monks who also harbor some hidden secrets. Julien strikes up an unlikely friendship with a new student, Jean Bonnet, who is quiet, reserved, and brilliant. The boys' relationship deepens as they share their interests and collaborate on schoolwork. Over time, Julien starts noticing that Jean behaves differently compared to the other boys, leading to suspicions and an eventual discovery of Jean's Jewish identity.

Events outside the gates echo the grim realities of the ongoing war, casting a shadow on the sanctuary-like atmosphere of the school. Tensions rise as the outside world encroaches on the insulated lives of the students and teachers. The bond Julien and Jean share grows, and their friendship faces tests and strains brought on by the harsh circumstances surrounding them. As internecine conflicts and the pressures of the Nazi occupation tighten their grip, the young boys are forced to confront complex moral decisions, innocence, and the cruel consequences of betrayal. The narrative paints a poignant yet turbulent portrayal of loyalty, courage, and the cruelty inherent in human nature during treacherous times.