On the day of his execution, a convicted murderer seeks to confess. He is visited by an old friend, Spencer Tracy as Father Flanagan, who runs a home for indigent men in Omaha, Nebraska. When prison officials imply that the condemned man owes the state a debt, Flanagan witnesses the man’s diatribe describing his awful plight as a homeless and friendless boy who was a ward in state institutions. After the officials leave, Flanagan provides some comfort and wisdom. On the train back to Omaha, Flanagan is transformed in his humanitarian mission by revelations echoed in the condemned man’s litany of hardships suffered as a child, without friends or family, and 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 even the boys, to build a sanctuary that 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, a poolroom shark with a sharp tongue and a knack for trouble. His elder brother Joe Marsh, Edward Norris, is in prison for murder and asks Flanagan to take Whitey—a tough-talking hoodlum—into Boys Town. Joe escapes custody during transfer to federal prison, and Whitey stays, embracing the chance to belong.
Whitey settles in and soon runs for mayor of Boys Town, determined to win with his slogan, don’t be a sucker. The town’s political landscape shifts as Tony Ponessa, Gene Reynolds, a disabled boy, is the actual winner of the mayoral race. Whitey’s ambitions collide with Freddie Fuller, Frankie Thomas, the outgoing mayor, and tensions flare after Whitey’s outburst when the election results come in. To settle the mounting feuds, a boxing match is staged, and Freddie defeats Whitey in view of Father Flanagan and the rest of the boys.
Disheartened by the loss, Whitey leaves Boys Town. Pee Wee, Bobs Watson, the town mascot, catches up with him and pleads, “We’re going to be pals, ain’t we?” but Whitey, nearly in tears, refuses and pushes the child away. He storms across the highway as Pee Wee, crying, wanders into the road, and is struck by a car. Overcome with guilt, Whitey wanders downtown Omaha and unexpectedly meets his brother Joe, who shoots him in the leg by mistake. Joe ferries Whitey to a church, calls Flanagan anonymously, and Whitey is taken back to Boys Town. The sheriff arrives to take Whitey, but Flanagan offers to assume full responsibility for the boy.
Whitey initially stays silent about the robbery, having promised Joe not to inform on him, but he soon realizes that his silence could jeopardize Boys Town. He goes to Joe’s hideout, and Joe recognizes that Boys Town matters more than their feud. Joe protects Whitey until Flanagan and a group of boys arrive, and the criminals are recaptured. The town’s generosity surges with donations, and Whitey is embraced by the community as the new mayor by acclamation. Dave Morris resigns himself to debt as Flanagan outlines his ambitious plans to expand the sanctuary, continuing his lifelong mission to prove that every child can be helped and redeemed.
