The World War II U.S. Navy submarine commander P.J. Richardson (Clark Gable) has an obsession with the Japanese destroyer that had sunk his previous boat and three others in the Bungo Straits. He persuades the Navy Board to give him a new submarine command with the provision that his executive officer, also known as the XO or the “exec”, be someone who has just returned from active sea patrol. He is single-mindedly training the crew of his new boat, the USS Nerka, to return to the Bungo Straits and sink the destroyer, captained by a crafty ex-submariner, now destroyer captain, nicknamed Bungo Pete. Richardson’s executive officer, Lieutenant Jim Bledsoe (Burt Lancaster), is worried about the safety of his boat and his crew. Bledsoe also is seething with resentment at Richardson and the Navy leadership for denying him command of the boat which he believes should rightfully have been his.
Richardson begins to drill the crew on a rapid bow shot, during which the submarine shoots at a destroyer moving in for the kill “down the throat” (i.e., at its bow coming head-on), which is normally considered a desperation shot due to the extremely narrow profile of the target. He then bypasses one target only to take on a Japanese destroyer using the bow shot on which they have drilled. The crew becomes outraged when it becomes apparent that Richardson is choosing to avoid all legitimate targets in order to enter the Bungo Straits undetected in direct contradiction to mission orders, jeopardizing the boat and its crew merely to avenge the destroyed submarine. Soon after engaging Bungo Pete, they are attacked by aircraft that had been clearly alerted to their presence and had been waiting in ambush. They are forced to dive and barely escape destruction from depth charges. Three of the crew are killed, and Richardson suffers a skull fracture which incapacitates him. They are also almost hit by what they mistakenly believe is one of their own torpedoes doubling back on them. By sending up blankets, equipment, and the bodies of the dead, they convince the Japanese that the submarine has been sunk. Bledsoe uses Richardson’s incapacitation to assume command and as an excuse to return to Pearl Harbor.
While listening to Tokyo Rose proclaiming the sinking of their boat, they are mystified how the Japanese were able to identify the crew of the boat. They later realize the Japanese are collecting their garbage. Bledsoe then realizes additionally that the submarine now has a real advantage—the Japanese believe they are sunk and their source of intelligence has ended—and returns to the Bungo Straits to fight the Akikaze destroyer, which the submarine defeats only to be subjected again to a mystery torpedo. Richardson deduces that it was not the Akikaze alone which had been destroying the US submarines but a Japanese submarine working in concert with the destroyer. He orders the boat into a dive just seconds before a Japanese torpedo shoots by. The US submarine then forces its adversary to surface and destroys it. The older submarine skipper thus achieves his revenge. The film ends with Richardson dying from his head injury and being buried at sea.