MacGyver is in the wilderness dodging rocket fire when a man draws a bead on him. Pete arrives to drop the man, then warns they are the only two left. He offers MacGyver a gun, but his friend turns it down. They head for a bridge where a silver box is hidden. One soldier is watching the bridge. MacGyver borrows Pete's rifle and uses a shoelace to rig it to fire after a piece of paper he's set up burns through. A woman in soldier gear spots the mechanism and walks away. Pete and MacGyver move through the brush and approach the bridge when the soldier leaves to investigate. MacGyver gets the box from beneath the bridge, but the woman opens fire and Pete collapses. MacGyver emerges and the woman shoots him in the chest. The woman whistles a signal and everyone gets up: the entire thing is a Bushmaster practice wargame.
The participating teams return to the airport and the Bushmaster sponsor, Jeff Moore of the Moore Corporation. MacGyver offers his congratulations to the woman, Kelly. Pete talks to Jeff Moore, the man in charge, who explains that Kelly is the daughter of Joe Henderson, the reigning Bushmaster champ and Jeff's top pilot. Jeff explains that Joe's plane went down over San Perez. The government is holding Joe as a spy, and Jeff hasn't had the heart to tell Kelly yet. Jeff finally explains to her what happened. At the Phoenix Foundation, Jeff confirms that Joe will be tried and executed in two days, and he wants Pete to put together a rescue team. Pete tells him that MacGyver's his man.
Later at the airport, Jeff tells Kelly to go home, but she wonders if he cares about his employees. MacGyver and Pete are going over the aerial maps and Kelly secretly watches them. Lt. Raoul Para, Joe's public defender, will meet MacGyver at a church. Jeff insists on flying MacGyver in himself. However, Kelly emerges from the rear cargo hold and makes the jump before they can stop her. MacGyver jumps after her and on the ground, warns her it isn't a game. Kelly notes that MacGyver doesn't have any weapons, and insists that she can handle the situation with the weapons she brought. They catch a passing bus and head into town. Meanwhile, Lt. Para meets with General Sanchez, who is handling Joe's case. Sanchez confirms they have planted evidence confirming Joe's guilt. Joe is brought in and Salazar asks for a taped confession in return for a mere 20-year sentence, rather than execution. Salazar gives him until the next morning to decide.
On the bus, Kelly comments that it seems too easy. They come to a roadblock and Kelly reveals that she doesn’t have her papers. MacGyver tells her to slip out the back while he distracts the guards, led by Lt. Barbero. The lieutenant is suspicious, and his men shoot a peasant. Kelly sees them and screams, and Barbero and his men arrest her and MacGyver when he comes to her aid. MacGyver tries to bluff it out, but when Barbero finds all of the weapons in Kelly’s pack he is sure they’re enemy spies. He takes them back to his tent and demands answers. Kelly insists they’re not revolutionaries but can’t account for their presence. MacGyver grabs a handful of sand and throws it into Barbero’s desk fan, blinding him and his man long enough for them to escape. They take refuge in an auto scrapyard and MacGyver says they need to wait until dark until he meets his contact. As they wait, they chat about Kelly’s family life and she admits she’s an only child. MacGyver wonders whether she’s there as Joe’s son or daughter.
Salazar berates Barbero for letting the prisoners escape, and Lt. Para suggests that they capture them and use them as leverage to demoralize Joe.
That night, MacGyver and Kelly go to the rendezvous spot, a local church, and meet with Lt. Para, his contact. Para warns that he can’t take Kelly in and it’s risky enough to take MacGyver in. Kelly insists that she needs to prove she can be a son, even though Joe never said it. She wants to prove herself and save her father, but MacGyver convinces her to stay at the church. Para takes MacGyver out of the church… and turns him over to the soldiers.
Joe is chasing off a rat when the soldiers bring MacGyver in. MacGyver identifies himself and warns Joe that Kelly stowed away. Meanwhile, Para suggests to Salazar that he put pressure on Joe now that his rescuer has been captured, and offers to visit Joe and MacGyver in their cell. Para meets with them and explains his plan to slip plastique through the window when the guard goes on patrol. MacGyver warns that it’ll be too loud and asks Para to bring him a canister of freon gas from a refrigerator in the kitchen. He plans to use it to freeze the lock and quietly break it. However, once Para leaves, Barbero and his men board up the barred windows as an extra security precaution. As they wait for sunrise, MacGyver uses a piece of string to capture the rat in Joe’s cell. Para returns and spots the boarded up windows, and then gets close enough to whisper to the prisoners. MacGyver sends the rat out through a drainage pipe, and has Para tie the string to the freon canister so he can pull it back in. MacGyver then freezes the lock bolt and breaks it off.
MacGyver and Joe lure the guard toward the door and knock him out, then head for the church. Joe’s injured leg slows him down but they make it just as Kelly is preparing to go look for them. Father and daughter are reunited. The soldiers discover they’ve escaped and begin searching the city. MacGyver figures the roads will be blocked but spots a railroad track.
Barbero finally reports his newest failure to a furious Salazar, who guns him down and tells his men to find the escapees.
MacGyver finds an abandoned jeep in the scrapyard and plans to put it on the railroad tracks. There are bullet holes in the radiator and MacGyver seals them by turning on the engine and pouring egg whites into the radiator. Meanwhile, Kelly admits that she was trying to prove herself and Joe says it isn’t necessary. Once the jeep is working, they put it on the tracks and drive out of town. The soldiers spot them and Salazar and his men give chase. The escapees head for the bridge leading over the river to their rendezvous with the helicopter. Salazar closes in and MacGyver borrows Kelly’s weapons, grenades, and miniflares. He puts them in a gas can, puts a rag in the mouth of the can, and then ignites it by running a metal rod along the tracks as they travel. MacGyver throws the can at Salazar and the explosion knocks his jeep over. The trio gets over the bridge and meets with the helicopter, making their escape.
Later, MacGyver, Pete, and Jeff go to the hangar to meet with Kelly and Joe for dinner. Salazar has fled the country and a new government will be taking power. Kelly is now wearing a dress, and Joe insists that it’s up to her if she plays in the Bushmaster competition.