In Barraca, Central America, rebels are driving across the countryside lead by Santina. In the back of one truck are Pete Thornton and Sister Clara. The convoy pulls into the rebel camp and Pete insists that Clara was only trying to help a dying man. Santina informs them the man was a traitor, and that her commander, Rafael, will want to know how they were connected with the man, Enrique. They're lead away and Santina wonders why Enrique betrayed them. Pete and Sister Clara are tied up inside a tent and Clara assures Pete that the underground saw them captured and will get word out. Pete warns that the U.S. can't be seen to be involved and the peace talks are taking place the next night with the country's president, Montoya. Clara explains that Enrique told her the rebels placed a bomb in the Presidential palace that will go off the next night.
MacGyver goes to see Jack Dalton at his new air and sea shipping firm. Jack is loading up his new seaplane with frozen food for San Clemente. MacGyver asks Jack for a favor: he needs his help going into Barraca to rescue Pete.
As they fly to Barraca, MacGyver is working on a garage door opener that will let them turn the plane on from a distance. MacGyver notes that Jack traded for missile launchers and Jack suggests that they go in as arms dealers and MacGyver will get them out.
Rafael arrives at the rebel camp and speaks out against the dictator Montoya. He examines Enrique's body briefly and Santina explains that she captured Clara and Pete. Rafael suspects that Pete is a spy because the Phoenix Foundation works with the U.S. government. Santina wonders how Enrique could be a traitor and Rafael admits that some are weak but they're strong.
Jack and MacGyver approach the coast of Barraca and MacGyver dresses up as an arms dealer.
Rafael goes to see the prisoners and demands to know what Pete is doing in the country. He insists he's just there to get the sisters out but Rafael doesn't believe him. When they refuse to tell him what Enrique says, Sanford tells them they can talk or they can die.
MacGyver finally tells Jack that they're helping to rescue a nun. Jack is none too thrilled.
Santina and Rafael take Clara and Pete to a levee and Rafael gives them one last chance to speak. When Pete refuses, Rafael shoots him in the shoulder and tells Sister Clara to decide. She finally tells him that Enrique told her about the bomb, but admits that she didn't have a chance to tell anyone else. They're interrupted when Jack and MacGyver land nearby. The rebels take Clara and Pete back to the tent while Rafael and Santina go to greet the plane. MacGyver hooks up the garage door opener to the plane's ignition They then introduce themselves as arms dealers and show themselves the missile launchers. Santina knows how to use them and blows up a nearby jeep. Rafael places an order and invites them into the camp for a celebratory drink.
In the tent, Pete wonders if MacGyver might be in the plane.
As Santina escorts MacGyver into the camp, she says that she has no fondness for arms dealers, like the ones who sold the weapons that killed her parents. MacGyver asks for a place to freshen up and she directs him to a spot near the ammo dump. Once she's gone, MacGyver spots the guarded tent and sneaks around to the back. He finds Pete and Clara and cuts them free. He tells Clara to call the guard in and then waits to the side. When the man comes in, MacGyver knocks him out and then throws an oil lamp into the nearby ammo dump to create a diversion. Rafael hears the noise and Jack knocks him out. Santina runs to investigate MacGyver and Jack join up and MacGyver activates the plane by remote. As they fly away, the rebels open fire and score several hits. The plane lifts off but soon starts to go down as they lose oil pressure. One of Santina's lookouts watches as they go down, landing on a stream in a nearby forest. They come to an abrupt stop as rocks rip open one of the pontoons.
As they tend to Pete's wound, Clara and Pete tell them about the bomb. They have less than six hours until the bomb goes off and kills President Montoya. MacGyver tries to radio out but the mountains are too high. They overhear the lookout calling in to Santina and telling her where they landed. Santina says they'll be there in three hours. Jack and MacGyver realize they have a lot of work to do.
Santina tells Rafael the good news and he prepares to move out with his men.
MacGyver comes up with a plan to melt the life jackets to repair the gash in the pontoon. He calls Clara to the side and gets her to tell him how bad Pete is. She explains what happened and that Rafael shot Enrique when he threatened his plans.
At the camp, Rafael gets increasingly anxious and begins to worry about how MacGyver and the others threaten his plans. Santina notices that he's more concerned about himself than the revolution. As they drive cross country, the jeep becomes trapped in mud and Rafael snaps at the supposed incompetence of Santina's people. He insists on going ahead on foot.
MacGyver and Jack complete the repairs and MacGyver tries to reassure Pete. Pete tells MacGyver that he's honored to be MacGyver's friend and then passes out. Sister Clara warns that there's nothing more they can do unless they get Pete to a hospital. They load up the plane but MacGyver realizes they don't have enough runway. He ties the plane to a tree and tells Jack to rev up the engines. However, Jack warns that it won't be enough and comments it'd take a rocket to get enough liftoff. MacGyver seizes on the idea and suggests they use the missile launchers.
As they trek across the countryside, Santina suggests that they offer the fugitives a chance to surrender via the radio. He refuses to consider it so she goes behind his back and contacts MacGyver to offer a surrender. MacGyver doesn't believe it and warns that Rafael is only interested in it for himself. He warns her that Rafael shot Enrique in the back, and she might have to watch her own back. She talks to Rafael, suggesting they approach with caution. Rafael refuses to listen to her and threatens to take away her command if she doesn't obey.
MacGyver rigs a triggering device to fire both missiles simultaneously, while Jack makes an anchor out of a rope and a log and fastens it with a slipknot. Rafael and the others come into sight and prepare to fire a mortar to take out the plane. Jack and MacGyver work to complete the launching assembly while Clara warns that Pete doesn't have much time. Rafael's man misses with the first shot and he angrily kicks him to the ground. Jack starts up the plane while Santina snaps at him and tells him they have no mortar rounds. She leads her men toward the plane while it hits the end of the anchor rope. When they hit maximum RPM, MacGyver tries to release the anchor. It doesn't come loose and he's forced to crawl down and cut the line. The plane heads down the stream out of range of Santina's men. MacGyver hangs on as Jack triggers the missiles and the plane lifts off. Rafael demands to know why Santina failed and she orders her men to take Rafael away as a traitor to the revolution.
As they clear the mountains, Clara uses the radio to call the Presidential palace and warn them about the bomb. Pete wonders where MacGyver is and Jack spares him the news that MacGyver is still holding onto the bottom of the plane.
Later, MacGyver, Jack, and a recovered Pete are back at the Phoenix Foundation. Santina has become instrumental in the peace talks and negotiated the first free elections. Jack makes sure that Pete is feeling better... and then gives him the bill for the repairs to his plane before making a hasty exit.