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On the day that Dave Morris returns to Boys Town after a year-long rest, Father Edward J. Flanagan is forced to admit to his old friend that the facility's newly built dormitories do not have the $200,000 cash needed to support their $300,000 bank loan. Dave gruffly pretends to be disgusted, but immediately starts fundraising. Meanwhile, Flanagan is called away to the trial of Ted Martley, a bitter, bedridden young boy accused of murdering a guard at Marysport reformatory. Ted, who is found guilty because he will not defend himself, tells Flanagan that the guard broke his back, thus causing Ted's paralysis. Members of the parole board ask Flanagan to take Ted to Boys Town, and Flanagan promises Ted that he will never see a doctor unless he wants to. At Boys Town, Flanagan asks his protégé, Whitey Marsh, to befriend Ted and broods about the brutality of a place like Marysport. Ted doesn't respond to Whitey or the other boys until one afternoon when Whitey brings a little dog into Ted's infirmary room. Unknown to Whitey, the dog, "Beau Hunk," belongs to Mr & Mrs. Maitland, visiting members of the parole board. When Whitey finds out, he apologizes and offers to buy the dog, and the Maitlands are so impressed that they ask to adopt Whitey, who reminds them of their recently deceased son. Flanagan doesn't want Whitey to go, but insists on letting him make up his own mind. Thinking that Flanagan wants him to leave, Whitey sadly agrees to the adoption and promises Ted that he will look up Miles Feneley, a friend at the Marysport reformatory. At the Maitlands', Whitey is given everything a teenaged boy could want, but does not feel at home. Meanwhile, at Boys Town, Ted is examined by a specialist who advises a difficult and painful operation. Ted is reluctant until Flanagan promises that he will be at his side during the operation. The next day, Whitey tries to see Miles, but a cruel guard warns him to keep away. As Whitey drives off, tough little Flip Brier escapes from the reformatory by hiding on the running board of Whitey's car. After Flip shows Whitey scars he received from whippings by the guards, Whitey decides to hide him while he contacts Flanagan. When Whitey leaves Flip alone for a few minutes, Flip robs a gas station. As he is about to rob a pawnshop, Whitey finds him and makes the pawnbroker think that it is a joke until the man sees a gun that Whitey has taken away from Flip. When Whitey discovers that Flip had gotten the gun duriing the gas station robbery, he is furious and is about to return it when they are stopped by the police. Mr. Maitland is summoned to the police station and, although he is sympathetic to Whitey, he thinks that Flip is thoroughly bad. When Whitey invokes Flanagan's philosophy that there is no such thing as a bad boy, Maitland becomes angry, and Whitey accepts jail rather than go home. At Marysport, Flip and Whitey are confined to "solitary row," where they see a boy drop over dead. The superindendant tries to convince them that the boy, who they learn was Miles, died of heart failure and warns Whitey not to make trouble. A few days later, Flanagan arrives to see Whitey and convinces the superintendent that he will fight, if necessary, to see the boy. Flanagan tells Whitey that he is proud that he tried to help Flip and Miles' mother begs the priest not to leave until Marysport is cleaned up. After an impassioned plea to the parole board, Marysport is soon reformed and Flanagan is able to return to Boys Town with Flip and Whitey, who tells the Maitlands that he no longer wants to stay with them. At Boys Town, Ted refuses to speak to Flanagan because of his absence during the operation. Flanagan becomes even more discouraged when Dave tells him that the bank has padlocked the unfinished dormitories. Learning about the finaicial problems, Whitey calls Maitland on his ham radio set and begs to go back, thinking that Maitland can help Flanagan financially, but Maitland coldly refuses. At an assembly, Flanagan says that he is the only person ever to fail Boys Town, and while he is speaking, a truck accidentally hits and kills Beau Hunk. Flanagan then sadly relates the news to Ted, who haltingly walks to the dog's funeral, during which the Maitlands arrive and tell Flanagan about Whitey's self-sacrifice. Maitland says he now knows that Boys Town must be saved and offers to help. At graduation, Whitey receives his diploma as the Maitlands sit hand-in-hand with a recuperated Ted.