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At night, in a quiet bay in the South Pacific, submarine officer "Duke" Gifford watches as a group of children and nuns is loaded onto rafts and transported aboard the submarine Thunderfish . While the children, which include a newborn infant nicknamed "Butch," are fed, a Japanese aircraft carrier is sighted, and the crew springs to action. Although the American torpedoes hit the enemy ship, they fail to fire, and the Japanese, now alerted to the submarine's presence, attack. The crew of the Thunderfish evades the enemy depth charges and sets course for Pearl Harbor. In the quiet that follows, Capt. "Pop" Perry asks Duke if he has heard from his ex-wife, Mary Stuart, who is now living in Honolulu. Duke reminisces about their divorce, blaming his dedication to work for the fact that he was at sea for both the birth and death of their son. After the Thunderfish arrives in port, Duke visits Butch at the hospital and by accident, encounters Mary, who is now a Navy nurse. The two still care deeply for each other, and share a passionate kiss, but when Duke asks if they can make a fresh start, Mary replies that she has a date with Navy pilot Bob Perry, Pop's brother. Later, Duke, Pop, Mary and Bob encounter one another at same restaurant. Bob, who has always felt overshadowed by Duke's exploits, announces that he and Mary are engaged to be married. Although Mary admits that she has not actually consented, when Duke tries to force a confrontation, she leaves with Bob. Duke follows with flowers, and he and Mary talk about their marriage, but before he can finish, Duke is summoned to settle a dispute between some of his crew and a group of Hawaiians. After the conflict is resolved satisfactorily, the Thunderfish is sent back to sea, where the crew again experiences problems with defective torpedoes. Pop is invited to go ashore and help fix the problem, and recommends Duke to head the next patrol. Before they return to port, they spot an enemy freighter. When the torpedoes again fail to explode, the Japanese ship runs up a white flag. Although he is puzzled by the action, Pop orders the submarine to surface and approach the vessel. The ship is a decoy, however, and opens fire on the Thunderfish . Although he knows he will not be able to get below deck in time, the wounded Pop orders the submarine to submerge. Then, under orders from the angry Duke, the crew rams the Japanese ship and sinks it. The crew heads home in their badly damaged submarine, and after a investigation, a service is held for Pop, whose body was never recovered. Bob believes that Duke gave the order to submerge and accuses him of trying to be a hero. Duke explains what really happened, but when Mary tries to sympathize with him, Duke rejects her efforts and adds that his only concern is keeping the crew of the Thunderfish together. After making his case to the commander, Duke and his men work to solve the torpedo problems and eventually achieve success with a new type of firing pin. One day, Duke invites Mary to dinner, but she declines, explaining that their relationship is doomed to fail because he will not let her comfort him when things go wrong. Nursing commander Steele, having overheard the conversation, advises Mary to take Duke as he is. Mary and Duke's problems are still unresolved when the Thunderfish again puts to sea. While tracking down the source of some major explosions, the crew happens upon the Japanese fleet heading for Leyte. Although it will put themselves in great danger, Duke orders the radio man to alert the American forces. They then fire all available torpedoes and, while battered by depth charges, destroy an aircraft carrier. After the U.S. attack begins, Thunderfish is asked to help rescue downed flyers. Under attack from Japanese planes, the men enact the rescues, and Duke is wounded while rescuing Bob. When they again dock in Pearl Harbor, Mary is waiting for Duke, and together they head for the hospital to adopt Butch.