In October 1942, ComSubPac directs the American submarine Greyfish, commanded by Lt. Cmdr. Barney Doyle Barney Doyle, to intercept a Japanese convoy that includes the Shinaru, one of the aircraft carriers that led the attack on Pearl Harbor. The escort also guards a transport ship carrying American prisoners from an internment camp in the Philippines where his wife Dede Doyle and child were being held. Doyle's second-in-command, Lt. Archer 'Archie' Sloan [Ernest Borgnine] tries to persuade him to let Sloan handle the torpedo run, sparing Doyle direct responsibility for his family’s possible death.
As the chase tightens, Sloan urges caution; the convoy’s proximity to the carrier Yoshida Maru presses Doyle into a difficult choice. Doyle fires his torpedoes, hoping to miss the carrier and strike the transport instead. Carefully counting the seconds, they realize one of their torpedoes has indeed hit the transport. Hoping to lure the submarine to the surface, the Japanese make no attempt to rescue the survivors. Through the periscope, Doyle can see women and children grasping for pieces of floating wreckage. So as not to endanger his crew, he is forced to leave the prisoners to die.
Doyle follows the Shinaru into Tokyo Bay, but fails to sink it. After surviving a relentless bombardment of depth charges, the Greyfish returns to base at Pearl Harbor. While there, Sloan meets with Admiral Setton [Philip Ober] and accepts Sloan's assessment that, despite feeling intense guilt for the civilian transport's destruction, he should be promoted and given his own command someday. He refuses on the grounds he believes Doyle is still fit for command and wishes to remain as his second-in-command. Setton then agrees to give the Greyfish “one more trip” to try to sink the Shinaru - but on the condition that Sloan must take the promotion if Doyle fails.
Yet when the Greyfish is reassigned to a quiet, out-of-the-way patrol area off the Alaskan coast, Doyle suspects betrayal by both Setton and Sloan, and reveals that he knew about the latter's offer of his own command all along. Then word arrives that the Shinaru is heading for Japanese-occupied Kiska Harbor, and the Greyfish sails toward the harbor.
An initial encounter with the Shinaru leaves the submarine’s periscope and radio antenna damaged, forcing Doyle to improvise a second, almost blind attack with little chance of success. After firing torpedoes, the Greyfish is driven to the ocean floor by a heavy depth-charge attack. The crew members use Momsen lungs to escape their doomed submarine. When they reach the surface, they are picked up by another American submarine, the Bluefin, captained by William Schallert. Doyle asks the Bluefin’s captain for confirmation that they hit the Shinaru. The captain looks through the periscope, shares the view briefly with Doyle and Sloan, and then, over the intercom, describes the carrier’s sinking for Doyle’s crew.
