The story opens when a convicted murderer asks to make his confession on the day of his execution. The condemned man is visited by an old friend, Father Flanagan (Spencer Tracy) who runs a home for indigent men in Omaha, Nebraska. When the prison officials suggest that the condemned man owes the state a debt, Father Flanagan witnesses the condemned man’s diatribe to prison officials and a reporter that describes his awful plight as a homeless and friendless boy who was a ward in state institutions. After the convicted man asks the officials to leave, Father Flanagan provides some comfort and wisdom. On the train back to Omaha, Father Flanagan is transformed in his humanitarian mission by revelations (echoed in the words) imparted by the condemned man’s litany of hardships experienced as a child without friends or family as a ward of the state.
Father Flanagan believes there is no such thing as a bad boy and spends his life attempting to prove it. He battles indifference, the legal system, and often the boys themselves, to build a sanctuary which he calls Boys Town. The boys have their own government, make their own rules, and dish out their own punishment. One boy, Whitey Marsh (Mickey Rooney) is as much as anyone can handle. Whitey’s older brother, in prison for murder, asks Father Flanagan to take Whitey (himself a poolroom shark and tough talking hoodlum) to Boys Town. Whitey’s older brother escapes custody during transfer to federal prison. After thinking he has caused the death of a younger boy, Whitey leaves the un-fenced Boys Town and wanders the streets of town. Whitey is accused of bank robbery and murder on circumstantial evidence. Popular sentiment (stirred by sensationalized media reports headed by an unsympathetic newspaper owner) turns against Boys Town, and it seems likely the home will be permanently closed. Whitey joins his brother, but Father Flanagan rescues Whitey and helps capture the gang in the act of robbery. Whitey and Father Flanagan return to Boys Town.