The main part of the movie is framed by Tommy (David Duchovny) as an adult. He's supposed to take his son for a bike ride but is too late. It's clear he hasn't has much to do with his son over the years and his wife is not happy.
Then we move to when Tommy was twelve and his best friend is the retarded Pappass (Robin Williams, in a marvelous role) who is the janitor at the Catholic school. Tommy's dad is dead and his mom is depressed, but she managed to get him a scholarship at the school. When Tommy starts liking girls (Zelda Williams, daughter of Robin) and spending less time with him, Pappass steals the bike they've been saving for, and Tommy lies and says he stole it so Pappass doesn't go to jail. He's kicked out of the Catholic school and his mother puts herself into a coma in response. When his second-cousin shows up to send him off to military school, he consults "Lady" (Erykah Badu) who is in the House of D(etention) and she tells him to run. (Her pimp, Superfly, is played by Orlando Jones in an excellent cameo.)
He takes a plane to France and now, all these years later as an adult, decides to go back to NYC and tell the folks who helped him back then how it all worked out. He meets "Lady" out of jail and finds Pappass. His family comes along and they have their bike ride.