In the early months of the Second World War, Nazi Germany's Kriegsmarine sends out merchant raiders to attack Allied shipping. The Royal Navy responds with hunting groups whose mission is to stop them. The group that finds the heavily armed pocket battleship Admiral Graf Spee near South America is outgunned: Graf Spee is equipped with long-range 11-inch guns, while the British heavy cruiser Exeter has much lighter 8-inch guns, and the light cruisers Ajax and Achilles have 6-inch guns. Despite this, they go straight to the attack.
After a German U-boat drops off Nazi saboteurs, RCMP Corporal Wagner (Flynn) captures the leader, Colonel Hugo von Keller (Helmut Dantine), the only survivor after an avalanche wipes out the rest of the group. When left alone with the Canadian Mountie, von Keller discovers that Wagner speaks German and is of German ancestry, and tries to persuade his captor to help him. After being taken into custody, von Keller leads a jailbreak from a prisoner of war camp, enlisting other German soldiers in his escape. Wagner, seemingly under suspicion by the RCMP of being a Nazi sympathizer, is court martialed and contacted by Ernst Willis (Gene Lockhart), a real enemy agent, who hires him as a wilderness guide.
The Royal Navy is concerned about constant attacks on convoys by German submarines and having to keep "half the fleet" watching for the German battleship Tirpitz. The Tirpitz is 60 miles from the sea inside a Norwegian fjord and attempts by the Royal Air Force to sink her have failed. Commander Fraser (Mills) is determined to prove that an attack by human torpedoes is practical, despite scepticism from the higher echelons that such an operation would be feasible.
The film opens in 1991, with the funeral of a World War II veteran. The man's daughter Marie (Neve Campbell) delivers the eulogy to a church full of veterans who knew and loved her father, while her mother Ethel Ann (Shirley MacLaine) is sitting out on the church porch, smoking and nursing a hangover. When Ethel Ann begins acting strangely, only her friend Jack (Christopher Plummer) seems to understand why. It quickly emerges that there is a lot Marie does not know about her mother's past and the true story of her love life.
Loosely based on actual events during World War II, the film depicts real life German Captain Bernhard Rogge commanding the navy raider Atlantis, which from May 1940 to November 1941 sank 22 Allied merchant ships. The story alternates between scenes at the Admiralty and scenes at sea, particularly showing Captain Rogge's humanity and chivalrous conduct of his military engagements. Rogge was one of the few German flag rank officers who was not arrested by the Allies after the war, due to his conduct as a military officer. After eighteen months of successful raids, Atlantis was sunk on 22 November 1941 by the British cruiser Devonshire.
The story, loosely based on actual events, takes place in March 1943, when the Second World War was at its height. The cryptanalysts at Bletchley Park, Buckinghamshire, have a problem: the Nazi U-boats have changed one of their code reference books used for Enigma machine ciphers, leading to a blackout in the flow of vital naval signals intelligence. The British cryptanalysts have cracked the "Shark" cipher once before, and they need to do it again in order to keep track of U-boat locations.
Captain Karl Ehrlich (John Wayne) is the master of the elderly German steam freighter Ergenstrasse, in port at Sydney, Australia on the eve of the Second World War. Ehrlich is depicted as a patriot, a former career naval officer who lost his rank and position after falling out of favour with the current regime and refusing to support the Nazi Party. As his ship prepares for sea (or to be interned if war is declared) he meets with an old friend, British Commander Jeff Napier (David Farrar) and his fiancée Elsa Keller (Lana Turner).
A US Navy submarine, the USS Corsair, is operating in the North Atlantic, hunting German merchant raiders that are preying on Allied shipping. Its new executive officer, Lt. Ward Stewart (Tyrone Power), has been transferred back into submarines after commanding his own PT boat. At the submarine base in New London, Connecticut, he asks his new captain, Lt. Cmdr. Dewey Connors (Dana Andrews), for a weekend leave to settle his affairs before taking up his new assignment. On a train bound for Washington D.C., Stewart accidentally encounters New London school teacher Jean Hewlett (Anne Baxter) and her students. Despite her initial resistance to his efforts, he charms her and they fall in love.
The USS Tiger Shark is a U.S. Navy submarine on patrol in the Atlantic Ocean during World War II in August 1943. She receives orders to pick up survivors spotted adrift by a British PBY Catalina patrol plane. She retrieves three survivors – the British nurse Claire Paige (Olivia Williams) and two men, one of them wounded – from the British hospital ship Fort James, which had been sunk two days earlier; one of the survivors blames the sinking on a German U-boat that he briefly saw on the surface just before the Fort James suffered a torpedo hit. As they pick up the survivors, the crew of the Tiger Shark spots a German warship bearing down on them. The submarine has several encounters with the German warship and suffers damage from depth charges in the process. Later, the commanding officer of the Tiger Shark, Lieutenant Brice (Bruce Greenwood), discovers that the wounded survivor is actually a German prisoner-of-war, Bernard Schillings (Jonathan Hartman). Brice confronts him because he thinks Schillings has been making noises to betray the Tiger Shark 's position to the German warship. Brice shoots Schillings dead when the German panics and grabs a scalpel to defend himself.
The film begins shortly after the outbreak of World War II when Günther Prien reports to the Befehlshaber der U-Boote (BdU—supreme commander of the U-boat Arm) Karl Dönitz. Dönitz orders Prien as commander of U-47 to penetrate the Royal Navy's primary base at Scapa Flow to inflict as much damage as possible. Prien accomplishes his mission and receives a hero's welcome on his return.
Steve MacKendrick (Alan Ladd), nicknamed "Canada" because that is where he claims he is from, volunteers in 1940 for the British Army's paratroop school. He obviously has a good deal more background and leadership skills than he lets on. Canada tries to become better acquainted with a pretty parachute rigger named Penny Gardner (Susan Stephen). She is initially put off by his attitude, but they eventually start dating. Both Penny and his new commander, Major Snow (Leo Genn), see potential (and a mystery that does not add up) in him, despite his strong efforts to avoid assuming any responsibility. Canada turns down Snow's offer to send him to officer school.