In 1946, Mr. Wilson (Edward G. Robinson) of the United Nations War Crimes Commission is hunting for a Nazi fugitive Franz Kindler (Orson Welles), a war criminal who has erased all evidence which might identify him. Kindler has assumed a new identity, Charles Rankin, and has become a prep school teacher in a small town in the United States. He has married Mary Longstreet (Loretta Young), daughter of Supreme Court Justice Adam Longstreet (Philip Merivale).
Wilson releases Kindler's former associate Meinike (Konstantin Shayne), hoping the man will lead him to Kindler. Wilson follows Meinike to the town of Harper, Connecticut, but loses him before he meets with Kindler. When Kindler/Rankin and Meinike do meet, Meinike, who is repentant, begs Kindler to confess his crimes. Instead, Kindler strangles Meinike, who might expose him.
Eventually, Wilson deduces that Rankin is Kindler, but not having witnessed the meeting with Meinike, he has no proof. Only Mrs. Rankin knows that Meinike came to meet her husband. To get her to admit this, Wilson must convince her that her husband is a criminal – before Rankin decides to eliminate the threat to him by killing her.
Rankin's pose begins to unravel when Red, the family dog, discovers Meinike's body. To protect his secret, Rankin poisons Red.
Meanwhile, Mrs. Rankin begins to suspect her husband, but is too blinded by love to accept the facts. She is torn between her desire to learn the truth about him, and the idea of helping him create his new life. Mr. Wilson shows her graphic footage of Nazi concentration camps, and explains how Kindler/Rankin developed the idea of genocide. But not until Mary discovers Rankin's plot to kill her does she finally break down. In a tense moment, she dares Rankin to kill her. Rankin tries to, but is prevented by Wilson and Mary's brother Noah. Pursued by them, he flees into a church belfry, and falls to his death.