In the early 1970s, two bright but rebellious boys, Franis Doyle (Emile Hirsch) and Tim Sullivan (Kieran Culkin), are fighting the stultifying repression of their parish school. They fight boredom, hormones, unresponsive teachers and clueless families in their quest to find something meaningful. Francis is an exceptional artist. He fills his notebooks with comic-book imagery and creates a fictional universe of good and evil for the two boys. Foremost among the forces of evil is the stern and disapproving nun, Sister Assumpta (Jodie Foster), who rules their lives. She seizes their artwork one day, setting the boys on an obsessed trail of revenge that ultimately changes their lives.