The Dangerous Lives of Altar Boys (2002) on Netflix

In the Seventies, the fifteen years old troublemaker and leader altar boy Tim Sullivan and his three great friends, Francis Doyle, Wade Scalisi and Joey Anderson, study in a repressive Catholic school, and they hate their nun-teacher Sister Assumpta. Francis has a crush on Margie Flynn, 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.