In 1946, Mr. Wilson (Edward G. Robinson) of the United Nations War Crimes Commission is hunting for Nazi fugitive Franz Kindler (Orson Welles), a war criminal who has erased all evidence which might identify him, with no clue left to his identity except “a hobby that almost amounts to a mania—clocks.”
Wilson releases Kindler’s former associate Meinike (Konstantin Shayne), hoping the man will lead him to Kindler. Wilson follows Meinike to the United States, to the town of Harper, Connecticut, but loses him before he meets with Kindler. Kindler has assumed a new identity and is known locally as “Charles Rankin,” and has become a prep school teacher. He has married Mary Longstreet (Loretta Young), daughter of Supreme Court Justice Adam Longstreet (Philip Merivale), and is involved in repairing the town’s 300-year-old Habrecht-style clock mechanism with religious automata that crowns the belfry of a church in the town square.
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 Mary 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 further protect his secret, Rankin poisons Red.
Meanwhile, Mrs. Rankin begins to suspect her husband, but she is too blinded by love to accept the facts. She is torn between her desire to learn the truth concerning her husband as a possible murderous monster and the idea of helping him create his new life. Mr. Wilson shows her graphic footage of Nazi concentration camps and explains how Rankin, as Kindler, developed the idea of genocide.
Not until Mary discovers Rankin’s plot to kill her does she finally relent. In a tense moment, she dares Rankin to kill her. Rankin tries to, but he is prevented by Wilson and Mary’s brother Noah (Richard Long). Pursued by them, he flees into the church belfry, is impaled by the clock mechanism he has labored to repair, and falls to his death.