In 1973 a squad of nine Louisiana Army National Guard soldiers convene in a local bayou for weekend maneuvers. New to the squad is Corporal Hardin (Powers Boothe), a cynical transfer from the Texas Army National Guard. He soon becomes disgusted with the arrogant behavior and attitudes of the men. A happily-married chemical engineer in his civilian life, Hardin wants no part of a date with prostitutes which PFC Spencer (Keith Carradine) has arranged for himself and their squad-mates. Nevertheless, he hits it off with the amiable Spencer, and both find themselves to be the most level-headed soldiers in their squad.
The nine soldiers set out on patrol and soon get lost in the swamp. They come across a seemingly-abandoned campsite with several pirogues. To continue onward, the Guardsmen need the pirogues. The squad’s leader, Staff Sergeant Poole (Peter Coyote), orders the soldiers into three of the pirogues. As they set out across the bayou, a group of Cajun hunter-trappers return and yell at the soldiers for having taken their pirogues. In response, PFC Stuckey (Lewis Smith) fires blanks from his M-60 machine gun at the Cajuns. They return fire with live ammunition, killing Poole and sending the squad into a frenzy as they make their way toward cover.
Sgt. Casper (Les Lannom) – the strict, inexperienced, and unpopular second-in-command – orders the squad to continue their “mission.” They discover that Cpl. Reece (Fred Ward) has brought along a box of live ammunition for hunting purposes. Reece is forced at knife-point by Hardin to give up the live ammo, and Casper divides it evenly among the soldiers, in order to bolster their chances of defense. They reach the shack of a one-armed Cajun trapper-hunter (Brion James), who speaks only French. Casper has him arrested as a prisoner of war. The emotionally-unstable Cpl. Bowden (Alan Autry) uses gasoline to ignite some TNT inside the shack, blowing it up, along with numerous provisions of food, fresh water, guns, and ammunition.
The soldiers feel increasingly threatened. Hearing the barking of dogs, the Guardsmen presume they’re about to be rescued. The dogs, however, belong to the Cajuns, who are now stalking the soldiers because of Stuckey’s actions. The Guardsmen fend off the attacking dogs, only to find that lethal boobytraps have been set for them. Pvt. Cribbs (T.K. Carter) is killed when he trips a spear-bed built into a spring-released cradle-frame, impaling him. The squad camps for the night. Overnight, Bowden begins to have a serious mental breakdown, refusing to speak to anyone or move. The group decides to tie him up for the night. The following morning, Reece tortures the one-armed Cajun by dunking his head in a fetid pond. Hardin discovers this and tries to stop it. Both soldiers get in a fight to the death with bayonets. As the men fight, Hardin gains the upper hand, and to his surprise, the one-armed Cajun screams for Hardin to kill Reece. After Reece is killed, the one-armed Cajun escapes into the swamp. Stuckey, who was close friends with Reece, threatens to kill Hardin.
As a helicopter passes overhead, the soldiers frantically try to signal it. Rushing headlong into the swamp after the chopper as it moves onward, Stuckey sinks to his death in quicksand. Having no confidence in Casper after his inept leadership, Spencer relieves him of command. They split up to search for Stuckey. Instead, the group locates the murderous Cajuns: Spencer and Hardin shoot one of them dead. Casper throws a homemade grenade at the Cajuns to no avail, then fixes his bayonet to his rifle and charges at them. Both he and Simms are shot dead.
Spencer, Hardin, and the now-catatonic Bowden camp for the night. The following morning Hardin and Spencer are jolted awake by a freight train, and then realize that Bowden is missing. They move to the train tracks and find Bowden hanging dead from a bridge. The one-armed Cajun appears on the tracks overhead. In perfect English, he warns Spencer and Hardin to leave the Cajuns’ territory while they still can. He gives them directions on how to escape the bayou, since Hardin and Spencer saved him from physical assault by Simms and Reece.
Following the one-armed Cajun’s advice, Spencer and Hardin follow a dirt road and end up hitching a ride with a friendly Cajun couple. They are driven to a pig roast at a nearby Cajun village. As Spencer happily mixes with the villagers, a wary Hardin sees the arrival of the three hunter-trappers who massacred their squad. One of Hardin’s would-be-killers chases him into a shed and wounds him in the arm. Spencer suddenly shows up, firing blanks at the Cajun as a distraction, giving Hardin the chance to stab him in the groin. The other two Cajuns arrive, and Spencer runs, leading them away from the injured Hardin. Spencer, hiding around a corner, hits one of the Cajuns in the face with the butt of his M-16, knocking him out. The remaining Cajun gives chase, but as he is about to shoot Spencer, Hardin grabs him from behind. This gives Spencer the opportunity to stab him to death with his bayonet. Leaving behind the village, Spencer and Hardin slip away unseen into the swamp. As the duo moves into the swamp, another helicopter arrives overhead and seems to stay in the vicinity. They get back to the dirt road just in time to see a U.S. Army truck drive towards them. They look at each other, knowing they are finally safe.