It's 1941, most of the world is at war, and Rafe McCawley (BEN AFFLECK) and Danny Walker (JOSH HARTNETT) are lifelong friends who grew up together and are now pilots in the U.S. Army Air Corps. While Danny is somewhat reserved, Rafe is charmingly cocky, a factor that not only wins the heart of Navy nurse Evelyn Johnson (KATE BECKINSALE), but also draws the attention of James H. Doolittle (ALEC BALDWIN), a forty-five-year-old officer who informs the young pilot that he's been accepted to join Britain's RAF in fighting the Germans.
Thus, while Danny and his comrades, including Red (EWEN BREMNER), head off to be stationed in Pearl Harbor, as do Evelyn and fellow nurses Betty (JAMES KING), Barbara (CATHERINE KELLNER) and Sandra (JENNIFER GARNER), Rafe ends up in a European dogfight where he's shot down and reportedly killed in action.
As Danny comforts Evelyn in her time of grief over that news, little does anyone know that Japanese Admiral Isoroku Yamamoto (MAKO) is planning a surprise attack on the Pacific Fleet anchored at Pearl Harbor. That's despite the efforts of Navy Department cryptologist Captain Thurman (DAN AYKROYD) who tries to convince President Roosevelt (JON VOIGHT) and others that an attack may be imminent.
Danny and Evelyn unexpectedly become lovers, a point that becomes complicated when Rafe suddenly reappears on the scene. Before they can resolve their romantic triangle, however, the Japanese attack Pearl, and the three, among with many others including Doris "Dorie" Miller (CUBA GOODING, JR.), a navy cook, and Earl (TOM SIZEMORE), an airfield mechanic, find themselves suddenly thrust into WWII.
As Danny and Rafe eventually take to the air to battle the Japanese fighters and Evelyn tends to the many wounded who come streaming into her hospital, the three try to sort out their romantic quandary, all while dealing with the aftermath of the attack that includes Doolittle leading a top secret retaliatory mission over Tokyo.