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In 1942, in the Bungo Straits near the coast of Japan, a U.S. Naval submarine captained by Commander "P. J." Richardson is sunk by the Japanese destroyer Akikaze . Richardson, who is among the survivors, spends the next year stationed at Pearl Harbor, Hawaii. Learning from his yeoman, Mueller, that the fourth submarine sent into the Bungo Straits has been destroyed by the Akikaze , Richardson resolves to request a return to sea duty. Soon after, the submarine Nerka arrives at Pearl Harbor. Because the Nerka 's captain has been injured, the ship's executive officer, Lt. James Bledsoe, expects to assume command. After Bledsoe receives orders to remain "exec" to Richardson, who has been assigned to captain the Nerka , Bledsoe confronts Richardson at his home, but Richardson flatly refuses Bledsoe's demand to be relieved. After the Nerka returns to sea with its new captain, the crew is soon dismayed to learn they have been assigned to patrol Area 7, which contains the Bungo Straits. Richardson's demanding, precision drills heighten the crew's anxiety until Bledsoe informs them that their orders forbid them to enter the straits. After a week of intensive drilling, the crew responds excitedly when a Japanese submarine is sighted, but are perplexed when Richardson refuses to engage the enemy ship. During a rapid dive drill, sailor Russo is accidentally trapped on the deck while emptying garbage and barely survives. When Richardson questions Bledsoe about the laxness of the crew, the exec informs him that the men have lost their respect for him because of his refusal to attack the enemy. Richardson doubles the drills and, a few days later, when the Nerka sights a tanker and a destroyer, orders the submarine into combat. Under Richardson's guidance, the Nerka destroys the tanker from the surface, then purposely lures the destroyer toward the submarine, which then executes a precision shallow dive that allows the crew to shoot torpedoes directly into the enemy ship's bow. The crew are greatly cheered by their successful attack, but later confounded when Richardson purposely evades a Japanese convoy the next day. Suspicious when Richardson orders a change of course, Bledsoe discovers the commander is taking the Nerka into the Bungo Straits. When challenged, Richardson reminds Bledsoe that a captain has discretion to change orders if it becomes advantageous to do so. Richardson insists that the Nerka crew has proven their ability to master the tricky, dangerous "down-the-throat" bow shot that will be necessary to sink the Akikaze . Bledsoe angrily accuses Richardson of senselessly risking the lives of the crew and threatens to bring charges against him if he fails. Shortly after the crew has been informed of the change in orders, Lt. j.g. Gerald Cartwright and several officers propose to Bledsoe that he relieve Richardson. Although the officers cite naval regulations, Bledsoe instantly quashes the plan, telling them it is their duty to follow their captain where ever he leads them. After days of scouting, the Nerka sights the Akikaze escorting a supply convoy. The submarine lures the destroyer by sinking two freighter ships, but as the Akikaze closes in on the Nerka , enemy bomber planes attack, forcing Richardson to order an early dive. After the Nerka torpedoes just miss the Akikaze , a wild torpedo circles back toward the Nerka , forcing evasive maneuvers. The Akikaze then drops depth charges on the Nerka , causing damage in the forward torpedo room. Richardson investigates and is knocked unconscious when a series of depth charges explode simultaneously outside the submarine's hull. Upon reviving, Richardson orders the jettisoning of debris, including the bodies of the crew killed in the attack in hopes that the Akikaze will believe the submarine destroyed. The ruse works, but Richardson, Bledsoe and the men are puzzled by an indecipherable Morse code message heard just after the Akikaze ceases its attack. When Medic Hendrix states that Richardson has suffered a severe concussion that needs immediate care, the commander orders him not to reveal the information. Richardson summons Bledsoe, who is stunned when the commander directs him to resume their search for the Akikaze after two days of mandatory repairs. Bledsoe refuses, assumes command and orders the ship to return to Pearl Harbor. The crew is relieved to be returning to port, but are disturbed by Bledsoe's agitation. Two days later, in the officer's mess hall, Bledsoe and the others are startled when a broadcast by Tokyo Rose laments the loss of the Nerka and names several lost officers and men, calling Mueller "Kraut," a nickname recently applied to him by Cartwright, who wrote it on a scrap piece of paper. Bledsoe abruptly questions several members of the crew then visits the ailing Richardson, who deduces that Bledsoe intends to return to the straits. Bledsoe reveals that he has concluded that the Japanese have been able to locate the submarines because they have been retrieving the submarines' garbage sacks. Bledsoe points out that because the Japanese believe the Nerka destroyed, the submarine now has a legitimate attack advantage. Bledsoe then orders the Nerka back to the Bungo Straits in time to intercept the next supply convoy. As the submarine engages the freighter to draw in the Akikaze , Richardson slips in and out of consciousness, fretting over the Morse code signal. The Nerka crew successfully blow up the Akikaze using Richardson's shallow dive maneuver, but are confused when they detect a torpedo coming at them. Richardson then revives and orders the ship to crash dive, informing Bledsoe that the Morse code has emanated from a Japanese submarine working in tandem with the Akikaze . The Nerka evades the torpedo, then attempts to silently wait out the Japanese submarine while both are deep undersea. Knowing that waiting is a weak gamble, Richardson tells Bledsoe that with the Akikaze destroyed, the convoy's only defense is the submarine, so Bledsoe orders the Nerka to surface and attack the convoy, thus forcing the enemy submarine to the surface. The ploy works and Bledsoe turns over the helm to Richardson for the successful attack on the submarine. After the attack, Richardson collapses and later dies. Bledsoe then leads the burial at sea service for the Nerka 's commander.