InMajor Vic 'Deak' Deakins (John Travolta) and Captain Riley Hale (Christian Slater) are pilots in the United States Air Force. The film begins with a boxing match between the two, where Hale is knocked out by Deakins. After the match Hale gives the bet money of the match back to Deakins saying he had stolen it from his wallet. Later both the pilots are assigned to a top secret exercise on a B3 Stealth Bomber with two nuclear missiles on board. Deakins and Hale take off from Whiteman Air Force Base in the Bomber (a fictional advanced version of the actual B-2 Spirit stealth bomber) carrying the two live nuclear weapons on an evening exercise over Utah.

After successfully evading the radar of the airforce base during the exercise, Deakins has a friendly chat during which he distracts Hale to check their port-side window. At this point, he draws his gun to shoot Hale. A combat ensued on board the plane and Deakins successfully manages to safe-drop the nukes from the plane after ejecting Hale. When the airforce base regains radar contact with the plane, Deakins reports that "Hale's lost it. I'm bailing out" and ejects leaving the plane to crash on the mountain side over the Utah canyons.

Meanwhile, a Special Forces team is sent to recover the nukes. They do not find the nukes on board the plane and report a "Broken Arrow" (a situation where nuclear missiles are missing). The team is later killed while recovering the nukes in a canyon by rogue mercenaries led by Deakins. Deakins plans to sell the nukes on the black market to prospective terrorists.

Hale is alive and is found by Park Ranger Terry, whom he convinces after a standoff to help him track down Deakins and foil his plot. From here the plot thickens with Hale fighting Deakins inside an abandoned mine shaft. One of the nukes set off by Deakins explodes, but the blast is contained by the millions of tons of rock above the underground shaft. Hale and Terry survive. Later, Terry and Hale track down Deakins to a motor boat to be used for transporting the remaining nuke that Deakins reacquired. Terry hides in the boat and as the mercenaries ride away in it.

Hale deciphers that Deakins is transporting the nuke on board a train and sets off in a helicopter to find the rogue train and hunt down Deakins. On board the train Hale finds Terry. A gunfight ensues between Hale, Terry and Deakins' henchmen. Most of the henchmen are shot dead and one gets thrown out of the train after the spinning blades of a chopper cut through his chest. The train is set on fire when the one of the bullets hits a fuel barrel during the gunfight. Finally, Hale faces off against Deakins in hand-to-hand combat in the bogey containing the nuke. Hale manages to overcome Deakins' fighting tactics and retaliates with a foray of blows, which weakens Deakins. After leaving Deakins presumably out cold, he leaps out of the train with a remote and turns off the timer on the nuke which was set to blow off by Deakins, before the fight. At the same instant, a detached train car comes slamming into the bogey where the fight had ensued. Due to the impact from the collision, the disarmed nuke flies into Deakins and the entire train explodes.

Hale who survived finds a 20-dollar note fluttering on a twig in the debris of the train wreck (The same 20-dollar note he had stolen from Deakins). He then finds Terry and they formally introduce each other.

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