Rafe McCawley (Ben Affleck) and Danny Walker (Josh Hartnett) are childhood friends who both dream of flying. As the world becomes embroiled in World War II in the early 1940's, Rafe and Danny sign on with the United States armed forces, although America is still in an isolationist position. Eager to participate in combat, Rafe is compelled to join the British air fight against the Nazis, leaving his girlfriend, beautiful army nurse Evelyn Stewart (Kate Beckinsale) behind. When Evelyn and Danny are transferred to the military base at Pearl Harbor, Hawaii, they hear the news that Rafe has been shot down and killed. Hoping to move on after grieving, Danny and Evelyn find themselves in love. When Rafe returns alive, the three find themselves in an uncomfortable personal situation that is soon engulfed by the massive surprise attack on Pearl Harbor.

Putting aside their differences, Rafe and Danny join the desperate fight against the enemy invaders. The film's epic sweep intertwines Rafe and Danny's stories with the heroic efforts of such characters as "Dorrie" Miller (Cuba Gooding Jr.), a ship's cook turned fighter, Earl (Tom Sizemore), a courageous base mechanic, and Jimmy Doolittle (Alec Baldwin), the visionary pilot who would lead one of America's most famous counterattacks of the war. Dan Aykroyd also appears as the code breaking Captain Thurman and Jon Voight as President Franklin Roosevelt.