 In the Seventies, the fifteen years old troublemaker and leader altar boy Tim Sullivan (Kieran Culkin) and his three great friends, Francis Doyle (Emile Hirsch), Wade Scalisi (Jake Richardson and Joey Anderson (Tyler Long), study in a repressive Catholic school, and they hate their nun-teacher Sister Assumpta (Jodie Foster). Francis has a crush on Margie Flynn (Jena Malone), who has a dramatic secret in her life. They like to write a comic book called  The Atomic Trinity  and all of them have an alter-ego in their superheroes: Brakken (Francis), The Muscle/Skeleton Boy later (Tim), Captain Asskicker (Wade) and Major Screw (Joey), with Sorcerella (Margie) joining them later. Francis uses to fantasize reality with the fantastic situations the heroes face against the evil Nunzilla/Pegleg, a dark caricature of Sister Assumpta. The group plots an evil prank against Sister Assumpta, with tragic consequences.