Petty career crook John Sedley (Mickey Rourke) is called Johnny Handsome because of his deformed face. His knack for observing and planning gets him and his friend into a robbery of a collectable coin store with Sunny Boyd (Ellen Barkin) and Rafe Garrett (Lance Henriksen) but the job goes sideways. Rafe and Sunny double cross the others killing everyone else in the job but Johnny. Johnny goes to jail and is warned that since this is his second time convicted for a felony, the next time makes him a third-time loser and he will be given the maximum sentence. In jail Johnny is accosted and knifed by two other inmates and sent to the hospital where he is visited by Lt. A.Z. Drones (Morgan Freeman) who tells him that Rafe paid to have him killed and urges Johnny to give evidence to take him down. While Johnny recuperates an enlightened Dr. Steven Fisher (Forrest Whitaker) believes that if he can repair Johnny's cleft palette and reconstruct his face he can change his life because the world will see him in a different more positive way. Lt. Drones tears down the doctor's ideas insisting that someone who is bad will continue being bad regardless of his looks'. Johnny agrees to the medical procedures and has his impaired speech and face changed and reenters society with a parole agreeing to continue psychological observation from the doctor. Johnny gets a job on a construction crew where he meets Donna McCarty (Elizabeth McGovern) who sees something special in Johnny but he pushes her away planning his revenge on those crooks that have double crossed him. He approaches Rafe and Sunny with a job to rob the construction site and things go along fine until suspicions cause curiosity.