John Wayne stars as a Lt. Commander on the U.S. submarine Thunderfish, which is on patrol near an enemy-held island. When the crew finds Wayne emerging from the jungle with a baby in his arms, he explains how the baby reminds him of his own son who passed away and that he is divorced from navy nurse Patricia Neal, whom he still loves.
After a brief encounter with enemy cruisers, the sub returns to base where Wayne reunites with Pat, who is now engaged to Philip Carey, a navy pilot and the younger brother of the Thunderfish's skipper, Ward Bond. On a subsequent patrol, the Thunderfish is damaged by an armed decoy and Bond is fatally wounded. Rather than risk the lives of the crew, Wayne orders the sub to submerge, leaving Bond behind. Carey holds Wayne responsible for Bond's death, but Pat intervenes as she still has feelings for Wayne.
When Wayne takes command of the Thunderfish and successfully intercepts an enemy armada, alerts the base, and rescues several bailed-out pilots including Carey, he and his crew become heroes. As the sub returns from its successful mission, Wayne sees Pat waiting for him.