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On Christmas Eve, the submarine U.S.S. Copperfin leaves San Francisco Bay under sealed orders. Christmas morning, the crew, which includes Tommy Adams, a new recruit; Tin Can, a Greek American who fervently hates the Nazis; Wolf, who is always talking about his female conquests; Pills, a former science student who is now the medical officer; Mike, a quietly religious man; and Captain Cassidy, celebrates the holiday.
After twenty-four hours at sea, Cassidy opens the orders, which direct him to proceed to Tokyo, by way of the Aleutian Islands. As the submarine approaches the Aleutians, a plane is spotted overhead. It is an American plane carrying Raymond, a meteorologist, who is traveling with the crew to Tokyo. Then two Japanese planes are spotted, and a battle ensues. Both planes are shot down, but the pilot of one of them parachutes to safety. When Mike tries to help him out of the water, the pilot stabs him to death and is killed in turn by Tommy. Because he was slow to shoot the pilot, Tommy blames himself for Mike's death and volunteers to defuse an unexploded bomb that has lodged under the boat's deck.
After the bomb is successfully defused, the men bury Mike at sea. Tin Can does not attend the service, which infuriates the other men, but he explains that his favorite uncle, a philosopher, was killed by the Nazis, and every Allied death causes him great pain. As the submarine nears Tokyo Bay, Cassidy informs the men that the ship must negotiate the mine fields on the bay's perimeter. When a returning Japanese cruiser and two destroyers approach the bay, Cassidy decides to follow them into the bay and thus avoid the mines. That night, Wolf, Raymond and Sparks go ashore to make the observations necessary for a future air attack on Tokyo. While the men are away, Tommy is discovered to have a ruptured appendix, and Pills operates with the help of an instruction book and improvised scalpels.
When the men on shore finish their observations, Raymond, who was reared in Tokyo, broadcasts their findings in Japanese. Despite this precaution, the Japanese decide to investigate the broadcast location, and the men narrowly escape discovery. Using the radioed information, the air attack on Tokyo begins, and the men of the Copperfin watch it through their periscope. After the attack, the submarine again slips through the mine fields by following a Japanese ship. The submarine's position is later revealed when the crew torpedoes a Japanese aircraft carrier. Other Japanese ships bomb the Copperfin , which is badly damaged.
When the submarine is unable to evade the destroyer that is following it, Cassidy orders the men to attack. The destroyer is sunk, and the submarine heads back to San Francisco, where Cassidy's wife and children are waiting at the dock.