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In the South Pacific in 1942, U.S. Lt. Cmdr. Barney Doyle and the crew of the submarine Greyfish take part in an intensive hunt for the Japanese battle ship Shinaru , which led the attack on Pearl Harbor. In addition to the tensions brought about by the search, Barney is anxious for news on the disposition of his wife Jane and young daughter Dee Dee, who stayed in Manila after the invasion of the Philippines by the Japanese. Barney is plagued with guilt that he did not insist on sending Jane stateside when she demanded that the family remain together in the South Pacific. After the Greyfish successfully attacks a Japanese destroyer, Barney and his executive officer, Lt. Archer Sloan, receive news from the head of the Pacific Submarine Fleet, Adm. Samuel Setton, that all the Americans in the Philippines have been safely transferred as prisoners of war from Manila. The good news is short-lived, however, as Setton later forwards news that the Shinaru is reported to be returning to Tokyo Bay, with a defensive escort that includes the transport ship carrying the American POWs, including Jane and Dee Dee. As the submarine nearest to Tokyo Bay, the Greyfish is assigned to attack. Suspecting that the Shinaru intends to use the transport as a protective screen, Arch tries to dissuade Barney from going ahead with the mission, but Barney declares that he has no choice. When the Greyfish sights the convoy escorting the Shinaru , Barney begins his attack, after which the POW transport places itself between the Greyfish and the Shinaru . Arch pleads with Barney not to risk killing Jane and Dee Dee, but Barney proceeds with the attack. Although Barney attempts to fire underneath the transport, the torpedoes hit the ship, which then breaks up. Barney and Arch watch in dismay as the Japanese allow the survivors to thrash about, hoping to lure the Greyfish to the surface to rescue them. After Barney orders evasive action, the Greyfish departs for safe waters. Later, the Greyfish is summoned back to Pearl Harbor, but Barney refuses to return, pointing out that the ship still has sixteen unused torpedoes. In spite of Arch's uncertainty about continuing, Barney orders the Greyfish to trail the Shinaru at a safe distance. After the Shinaru and remnants of the convoy enter Tokyo Bay, Barney fires upon a tug pulling a protective webbing to enclose the harbor and uses the distraction of the sinking tug to slip into the bay. A Japanese destroyer detects the Greyfish in the bay, but Barney keeps the submarine precariously hidden in a mine field, and when the destroyer follows the submarine it is blown up. Barney then navigates the Greyfish through the mine field for a shot at the Shinaru , but its protective screen again places another ship between the submarine and its objective. After a second destroyer sets out in pursuit of the Greyfish , Barney pilots his ship back into the mine field for protection. Following the suggestion of Lt. Redley, a British officer stationed aboard the submarine, Barney detonates several mines to make the Japanese believe the Greyfish has been destroyed. When the destroyer returns to the harbor, Barney blows a hole in the protective webbing with the last of his torpedoes, enabling the Greyfish to escape. Exhausted, Barney orders the ship back to Pearl Harbor, then retires to his quarters where he sleeps for three days. Upon awakening, Barney asks Arch if he will report his three day loss of consciousness. Arch denies there was anything unusual in Barney's behavior. After the Greyfish returns to port, Barney immediately demands that the ship receive top priority to be repaired. The next day, Setton summons Arch to inform him that he has been promoted and is to receive his own command. Although pleased, Arch asks about the Greyfish and presses for Barney to have another opportunity to go after the Shinaru . Setton suggests that Barney is overdue for a desk position, then asks if Arch is covering for Barney. Arch admits that Barney blacked out for three days, but insists his commander is fit. When Arch refuses his command in order to remain with the Greyfish , Setton agrees to allow Barney one more mission. Partnered with another submarine, the Bluefin , the Greyfish heads back out to sea, but Barney is disturbed when he receives orders to patrol a trouble-free area near Kiska harbor. Suspicious that Arch may have criticized his handling of the previous mission, Barney questions Arch's loyalty. Later, Barney receives confirmation that the Shinaru has been sighted near Kiska. When Barney asks Arch whether he was offered his own command, Arch, stung by Barney's earlier doubts, refuses to explain. The Greyfish and Bluefin speed to Kiska, where extreme fog and rough seas prevent them from attacking the moored ships. When spotted by the Shinaru 's escort, the Greyfish dives for protection, but strikes a defensive cable of logs which tears off the ship's antennae and damages the radar. In the collision, Barney sustains a broken arm, but using sonar, the Greyfish detects that the Shinaru is weighing anchor. With an enemy destroyer bearing down on his damaged submarine, Barney asks Arch if they can make a sonar-only based attack. When Arch declares they will have only one shot, Barney allows Arch to fire upon the Shinaru . Just after launching its torpedoes at the battleship, the Greyfish is bombarded by depth charges from the destroyer and sinks to the bottom of the sea. Unable to signal the Bluefin , Barney is considering his options, when the Bluefin locates the sunken submarine and comes to its rescue. Using aqualungs, the crew of the Greyfish swim out of the submarine and are taken onboard the Bluefin , where Barney demands to know the outcome of their attack. Despite the heavy mist and smoke, Barney and Arch are relieved when they witness the sinking of the Shinaru .