During the Bosnian War, United States Navy flight officer Lieutenant Chris Burnett and pilot Lieutenant Jeremy Stackhouse are stationed on the aircraft carrier USS Carl Vinson in the Adriatic Sea. Burnett is preparing to leave the Navy, and clashes with his commanding officer, Admiral Reigart. On Christmas, Reigart assigns Burnett and Stackhouse to fly an aerial reconnaissance mission, which goes smoothly until they spot unusual activity in the demilitarized zone. Burnett persuades Stackhouse to fly their F/A-18F Super Hornet off-course for a closer look, unaware that they are photographing Serb Volunteer Guard soldiers burying massacred Bosnian Muslim civilians in mass graves. The local Bosnian Serb paramilitary commander, General Miroslav Lokar, is conducting a secret genocidal campaign against the Bosniak population, and orders the jet be shot down.
Attempting to outmaneuver Lokar's surface-to-air missiles, Burnett and Stackhouse's jet is hit, forcing them to eject. Lokar and his men find the injured Stackhouse, who is executed by Sasha, one of Lokar's right-hand men. Watching nearby, Burnett flees into the wilderness, and Lokar orders his deputy, Colonel Bazda, and Sasha to hunt him down. Burnett radios for help and receives an extraction point from Reigart, who is forced to stand down after Admiral Piquet, the commander of NATO naval forces in the region, warns him that rescuing Burnett in the demilitarized zone risks derailing the peace process. Burnett reaches the extraction point only to be informed that he must continue to another location, miles outside the demilitarized zone, in order to be rescued.
Spotting Bazda's patrol, Burnett falls into a mass grave, and hides under a dead body until the Serbs move on. To ensure Burnett's rescue, Reigart leaks news of the downed jet to the press, angering Piquet. Lokar realizes that the American jet's hard drive with the incriminating photographs may still be in the wreckage. Heading to the new extraction point, Burnett escapes Serb soldiers through a minefield. Pursued by Sasha, he encounters Bosniak guerrillas who offer him a ride to the town of Hač, which turns out to be a war zone. After the battle, Serb troops believe they have found Burnett's body, but Sasha realizes Burnett switched uniforms with a dead Serb guerrilla and escaped. The Serbs present the corpse wearing Burnett's uniform to the media, convincing NATO forces that Burnett has been killed, and the mission to rescue him is aborted just as he reaches the extraction point.
Realizing why the Serbs shot him down, Burnett remembers a statue of an angel near where his ejection seat landed, and returns to find it. He activates the seat's rescue beacon, notifying his carrier group that he is still alive, but also alerting the Serbs to his location. Knowing he risks being relieved of command, Reigart prepares a task force to rescue Burnett, in defiance of Piquet's orders. On the way to kill Burnett and recover his body, Bazda steps on a landmine; Sasha abandons him to his fate, and the explosion alerts Burnett that someone is approaching. Sasha finds the ejection seat, but is ambushed by Burnett, who fatally stabs him with a flare. Lokar arrives with armored vehicles and infantry, but is held off by Reigart's task force. Retrieving the hard drive, Burnett is successfully rescued.
The photographs of the mass grave lead to Lokar's arrest and conviction for war crimes including genocide. Reigart's actions result in him being relieved of command and retiring from service, and Burnett continues his career in the Navy.
Owen Wilson as Navy Pilot Lieutenant Chris 'Longhorn' Burnett
Gene Hackman as Rear Admiral Leslie McMahon Reigart
Gabriel Macht as Navy Pilot Lieutenant Jeremy 'Smoke' Stackhouse
Charles Malik Whitfield as Marine Captain Glen Rodway
David Keith as Master Chief Tom O'Malley
Olek Krupa as Serb General Miroslav Lokar
Joaquim de Almeida as Admiral Juan Miguel Piquet
Vladimir Mashkov as Serb Sniper Sasha Ivanic
Marko Igonda as Serb Colonel Viktor Bazda
Eyal Podell as Petty Officer Kennedy
Laurence Mason as Captain Glen Brandon
Leon Russom as Ed Burnett
Geoffrey Pierson as Admiral Donnelly
Vladimir Oktasec as Serb President Petrovic
Salaetin Bilal as Muslim Guerilla Leader Ejup
Kamil Kollárik as Muslim Guerilla Babić
Aernout Van Lynden as Himself