Humphrey Bogart returns to Tokyo after the end of World War II, hoping to see if his pre-war bar and gambling joint, Tokyo Joe's, still stands. The place is surprisingly intact and is being run by his old friend Ito. Joe’s first shock comes when Ito reveals that his wife, Florence Marly Trina, is alive—she had not died in the war. She has divorced Joe and remarried Mark Landis, a lawyer working in the American occupation, and they have a seven-year-old daughter named Anya, who becomes a central figure in Joe’s emotional and legal reckoning.
To stay in Japan after his visitor’s permit expires, Joe aims to establish an airline freight franchise, and Ito introduces him to Baron Kimura, the former head of the Japanese secret police. Sessue Hayakawa Kimura agrees to finance a small airline that would carry frozen frogs for export to the Americas, but Joe suspects the venture may be a front for other shipments—penicillin, saccharine, and pearls. As the government stalls on permission, Kimura presses Joe to move forward, hinting at deeper interests behind the deal.
Kimura then presents Joe with surveillance from Japanese secret police files showing that Trina broadcast propaganda while she was naturalized as an American citizen, a treasonable offense in the eyes of the occupation authorities. When Joe confronts Trina, she explains that the broadcasts were a desperate move to protect her newborn child, and she reveals that Anya is Joe’s daughter. Faced with the choice, Joe agrees to proceed with the airline scheme to safeguard Trina, and he enlists Alexander Knox Mark Landis to help him, aiming to secure the necessary backing before his stay runs out.
Unbeknownst to them, Kimura’s true intent goes beyond business. He plans to smuggle in fugitive war criminals and leaders of the Black Dragon Society to fuel a covert anti-American movement, a plot the American occupation authorities are monitoring. They intend to arrest the conspirators when they land at Haneda, but Kimura learns that Joe has already met with the Americans. He raises the stakes by kidnapping Anya and demanding that the Japanese and their allies be delivered on a deadline, threatening the child’s safety.
With a plan in motion, Joe takes a flight with paying passengers toward the Army-designated strip, only to be hijacked by Japanese forces who divert the plane to a different airstrip at Okuma. The U.S. Army closes in, preventing a wider disaster, and they intervene just as the hijackers are cornered. Back at the bar, Ito reveals one final, grave truth: Anya is being held in a basement beneath the old hotel next door. Joe follows the trail into the dark, rescuing Anya, but is mortally wounded when Kimura shoots him while he carries the child to safety. American soldiers arrive moments later and kill Kimura, but Joe is carried out on a stretcher, his fate sealed by the injuries he sustains in the rescue.
