舞台はハワイ沖。アメリカをはじめとする世界各国の艦艇が集結して大規模な軍事演習が行われるなか、沖合に正体不明の巨大な物体が出現する。それは、地球からの友好的な呼びかけに応じて飛来したエイリアンの母船だった。しかし、呼びかけを行った科学者たちの意図とは裏腹に、エイリアンは次々と未知の武器を繰り出し、激しい攻撃を仕掛けてくる。その戦いの最前線に立たされたのは、演習に参加していた米海軍の新人将校アレックス・ホッパーと、彼がライバル心を燃やす自衛艦の指揮官ナガタだった。弱点も戦略も読めないエイリアンに対し、知力と体力の限りを尽くして精鋭たちは立ち向かう！

Maverick Navy Lieutenant Commander Tom Dodge will never be a textbook officer, but he's a brilliant seaman who's always wanted to command a nuclear submarine — he's been given one last chance to clean up his record. Unfortunately, Admiral Graham, his nemesis, would rather sink the fleet than give Dodge his own boat. So, Graham stacks the deck against him and assigns Dodge to the Stingray, a diesel-powered WW2 submarine that can barely keep afloat. To make matters worse, Dodge's crew is a collection of maladjusted, mistake-prone misfits. Then, he's tagged the "enemy" in a crucial war game, and ordered to take on the U.S. Navy's best.

Merchant Marine sailors Joe Rossi (Humphrey Bogart) and Steve Jarvis (Raymond Massey) are charged with getting a supply vessel to Russian allies as part of a sea convoy. When the group of ships comes under attack from a German U-boat, Rossi and Jarvis navigate through dangerous waters to evade Nazi naval forces. Though their mission across the Atlantic is extremely treacherous, they are motivated by the opportunity to strike back at the Germans, who sank one of their earlier ships.

This film shows the duties of a young British sailor, Lieutenant Ellison, as his submarine H.M. Artemis sails the pack ice north of Iceland to gather data to complete a scientific survey for the Hydrographic Department.