Lt. Daniel Kaffee (Tom Cruise) is a military lawyer defending two U.S. Marines charged with killing a fellow Marine at the Guantanamo Bay Naval Base in Cuba. Although Kaffee is known for seeking plea bargains, a fellow lawyer, Lt. Cdr. JoAnne Galloway (Demi Moore), convinces him that the accused marines were most likely carrying out an order from a commanding officer. Kaffee takes a risk by calling Col. Nathan R. Jessep (Jack Nicholson) to the stand in an effort to uncover the conspiracy.
After returning home from the Vietnam War, veteran Jacob Singer (Tim Robbins) struggles to maintain his sanity. Plagued by hallucinations and flashbacks, Singer rapidly falls apart as the world and people around him morph and twist into disturbing images. His girlfriend, Jezzie (Elizabeth Peña), and ex-wife, Sarah (Patricia Kalember), try to help, but to little avail. Even Singer’s chiropractor friend, Louis (Danny Aiello), fails to reach him as he descends into madness.
After the Cold War, a breakaway Russian republic with nuclear warheads becomes a possible worldwide threat. U.S. submarine Capt. Frank Ramsey (Gene Hackman) signs on a relatively green but highly recommended Lt. Cmdr. Ron Hunter (Denzel Washington) to the USS Alabama, which may be the only ship able to stop a possible Armageddon. When Ramsay insists that the Alabama must act aggressively, Hunter, fearing they will start rather than stop a disaster, leads a potential mutiny to stop him.