During World War II, Duke E. Gifford, played by John Wayne, is second in command of the USS Thunderfish, a submarine plagued by malfunctioning torpedoes. As he investigates the issue, he must also navigate his feelings for his ex-wife, Mary Stuart, a Navy nurse (Patricia Neal), who is now romantically involved with her brother-in-law, Lt. Bob Perry (Philip Carey). When Commander John "Pop" Perry is mortally wounded during a surface action, Duke takes command and leads the sub in a daring attack on a heavily armed Japanese freighter.