During World War II, the submarine USS Thunderfish, under the command of Duke E. Gifford John Wayne, is on a perilous mission to the Philippines to rescue a group of nuns and children, including a newborn infant nicknamed "Butch," and transport them to Pearl Harbor. On the way, the sub sights a Japanese aircraft carrier and attacks, but its torpedoes malfunction, exploding halfway to the target. Attacked and pursued by the carrier's escorting destroyers, Thunderfish manages to escape.
At Pearl Harbor, the ship's Executive Officer, Lieutenant Commander Duke E. Gifford, goes to visit Butch at the base hospital, and runs into his ex-wife, Mary Stuart Patricia Neal, a Navy nurse, and they kiss passionately. Mary is now romantically involved with Navy pilot Bob Perry [Philip Carey], Pop's younger brother. Duke pursues Mary anyway, but is sent to sea again before anything is settled.
As the sub returns from the patrol, they spot a Japanese freighter, but again their torpedoes fail to explode. The enemy ship raises the white flag, and Thunderfish surfaces and approaches. The freighter turns out to be a heavily armed Q-ship that opens fire on the sub. Mortally wounded, John "Pop" Perry [Ward Bond] orders the boat to crash dive, knowing that he will not be able to get below before she submerges.
Duke, now in command, orders a "battle surface" behind the ship. On surfacing, Gifford orders the deck guns and anti-aircraft guns, as well as numerous portable light and mountable heavy machine guns operated by the deck crew, to fire at will. After the Q-ship's bridge is disabled and the ship set afire, Duke orders flank speed, ramming the sub into the Japanese ship, holing and sinking the Q-ship.
Thunderfish limps home for repairs to her damaged bow. Back at Pearl Harbor, Bob Perry believes that Duke's order to dive the boat killed his brother, and he refuses to listen to Duke's explanation. Mary tries to comfort Duke, but he rejects her attempts, declaring he only did his duty and feels no regret.
Working with the sub base's torpedo specialists, Duke and the crew of the Thunderfish investigate why the torpedoes are not exploding. When they finally discover the answer, Duke goes to Mary to celebrate, but she rejects him. Since he would not let her into his life when he was at his lowest, she feels that they cannot have a real relationship. Her superior, Commander Steele, overhears the conversation and castigates Mary for throwing away her chance for happiness with Duke.
Once again Thunderfish heads to sea, this time as part of a scouting line searching for a Japanese fleet heading for Leyte to attack the American invasion force there. Thunderfish finds the enemy. Even though it will reveal their presence, Duke broadcasts the fleet's position. Once Pearl Harbor acknowledges the message, Duke salvoes his torpedoes and makes a run for it, throwing the attacking Japanese warships into chaos. Despite enduring a battering from Japanese depth charges, Thunderfish manages to sink a Japanese aircraft carrier.
In the next phase of the battle, American carrier aircraft arrive and attack the Japanese fleet. Thunderfish, now assigned to lifeguard duty, helps to rescue shot-down American flyers, and does so while under attack from Japanese fighters. While rescuing the wounded Bob Perry, the Chief of the Boat and Junior, a seaman from a Navy family, are killed and Duke is wounded by a strafing Japanese Zero.
When the Thunderfish returns to Pearl Harbor after the patrol, Mary is waiting for Duke. The two, reconciled, head to the hospital, intending to adopt Butch.
