MacGyver and Pete are in the wilderness dodging rocket fire and enemy soldiers. Their goal is a silver box hidden beneath a bridge. MacGyver borrows Pete's rifle, but rigs it to fire on an improvised timer to draw a guard away. Once the guard goes to investigate, MacGyver crawls under the bridge and grabs the box. Pete, standing guard, is shot by a woman watching from the brush. When MacGyver emerges, the woman shoots him as well, and then whistles, ending the Bushmaster competition.
The teams drive back to the Moore Corporation, where Jeff Moore is sponsoring the yearly event. The woman, Kelly, is the daughter of Joe Henderson, the reigning Bushmaster champ. Joe is also Moore's top pilot. Moore tells Pete and MacGyver that Joe's plane went down in the country of San Perez, and he is being held as a spy. Moore finally tells Moore what happened. They meet at the Phoenix Foundation after Moore has confirmed that Joe is to be given a show trial and then executed. Pete tells Moore that MacGyver will be going in single-handedly to rescue the pilot.
As the men make plans at Moore's hangar, Kelly comes in and insists on helping. Moore says they have everything in hand and tells her to go home. Instead, Kelly hides and watches them plan MacGyver's operation. He'll meet with Lt. Raoul Para, a sympathizer within the military government headed by General Salazar.
The next day, Moore himself flies MacGyver to San Perez. As MacGyver prepares to parachute in, Kelly emerges from the cargo hold and jumps out first. MacGyver goes after her and on the ground, tells her that it's not a game. Kelly wonders how MacGyver could handle the rescue, and reveals that she's brought a gun, grenades, and miniflares. MacGyver has no choice but to take her along with him. They catch a passing bus and go into the town where Salazar has his headquarters.
Lt. Para meets with Sanchez. The general admits that they've framed Joe. Salazar has the injured pilot brought in and offers to commute his sentence to 20 years if Joe gives him a taped confession. Joe has until the next morning to agree.
The bus comes to a roadblock, and Kelly admits that she forgot to bring her papers. MacGyver has her get out the back while he gets past the soldiers. Lt. Barbero, the man in charge, has the passengers disembark and checks their papers. One peasant can't account for himself, and Barbero's men shoot him. Kelly, seeing the execution, screams and the soldiers capture her. MacGyver tries to convince them she was just hiding because she lost her papers, but Barbero finds her pack containing weapons and believes they're rebels.
At Barbero's command tent, the lieutenant demands to know what they're doing in San Perez. Kelly insists they're not rebels, but can't explain the real reason they're there. When Barbero's man slams MacGyver to the floor, MacGyver grabs a handful of dirt and throws it into Barbero's desk fan. He and Kelly escape during the distraction and take refuge in a nearby auto junkyard. MacGyver says they need to wait until sunset so he can meet with Para. As they wait, MacGyver asks Kelly about her home life. Kelly admits she's an only child and always figured that Joe wanted a daughter. MacGyver wonders if she's there as Joe's daughter or son.
Salazar meets with Barbero and tells him to find the escapees. Para suggests that they capture them and use them to demoralize Joe, rather than shoot them on sight. Salazar agrees and tells Barbero to find MacGyver and Kelly.
Later, MacGyver and Kelly go to the nearby church and meet with Para. Para refuses to take Kelly into the compound where Joe is held, saying it's risky enough to smuggle MacGyver in. Kelly initially refuses, insisting she have the chance to prove herself, but MacGyver convinces her to stay behind. he leaves with Para, who immediately turns him over to the soldiers.
Joe is chasing a rat away from his meal when the soldiers throw MacGyver into the cell. MacGyver explains that he's there to rescue him and that Kelly came along.
Para goes to see Salazar and says that they can force Joe to confess now that his rescuer has been captured. Salazar agrees to let Para meet with the prisoners and convince them to confess. Para goes to the cell and tells them of his plan to smuggle plastique in through the bars on the window. MacGyver points out that it would be too noisy and comes up with an alternate plan: he asks Para to get him a freon cylinder from a refrigerator. Once Para smuggles it in through the window, MacGyver will freeze the lock, quietly, and they can make their escape. However, once Para leaves, Barbero and his men board up the window and MacGyver realizes they need an alternate plan.
During the night, MacGyver tries to capture the rat that has been plaguing Joe. He finally lassos it with a piece of twine. When Para arrives, MacGyver tells him to grab the rat as it comes out of the drainage pipe leading out of the cell. Para ties the twine to the freon cylinder and MacGyver pulls it back through to the cell. he then starts freezing the lock. It breaks and Joe and MacGyver slip out. When a guard goes by, they slam the door into his face, knocking him out, and head back to the junkyard.
Kelly is just getting ready to leave when the men find her. They go back to the junkyard where Joe's injured leg gives out entirely. They have no way to get to the rendezvous spot on foot. MacGyver spies a Jeep in the junkyard and a nearby set of railroad tracks and figures the soldiers will have established roadblocks, but overlooked the tracks.
Barbero tries to conceal the escape as long as possible, but Salazar finds out and has him shot for his incompetence. He orders his men to find the prisoners at all costs.
MacGyver repairs the Jeep's bullet-ridden radiator by dumping egg whites into it and letting them cook. Meanwhile, Kelly insists that she came to rescue Joe and prove herself to him, but Joe explains that he never wanted her to be anything other than herself. they get in the jeep and head down the tracks toward the rendezvous spot. Salazar's men spot them and report in, and the general and his men give chase. As they close in, MacGyver borrows Kelly's weapon stash, puts everything in a gas can, then ignites it and throw sit at Salazar's jeep. The general's vehicle goes off the road and the escapees get to the rendezvous and meet the helicopter.
Later, Pete and MacGyver meet with Moore and the Hendersons for dinner, while learning that Salazar has fled the country. Kelly is now wearing a dress and Pete wonders if she'll be in the next Bushmaster competition. Joe assures her that she can do whatever she wants.