In the country of Barraca in Central America, the rebel commander Santina has captured two traitors to the cause: Pete Thornton and Sister Clara. She takes them to her camp where Pete tries to explain that the nun only tried to help Enrique, a dying man. Santina explains that Enrique was a traitor and that her leader, Rafael, will want to know what Enrique told them. The two prisoners are held in a tent and Clara that the underground will notify the world they were captured. Pete warns that there are peace talks taking place between the rebels and the president, Montoya. Clara tells Pete that Enrique told her that the rebels planted a bomb in the Presidential palace and plan to set it off the next night during the peace talks.
MacGyver needs a plane to get into Barraca and has no choice but to seek the help of his old friend Jack Dalton. Jack is happy to help Pete out after all the favors he's asked for over the years. As they fly to Barraca, MacGyver rigs a garage door opener to the plane's ignition. He observes that Jack has bought some missile launchers and Jack explains that he bought them from one of his customers so that they can go in impersonating arms dealers. Once Jack gets them in, it'll be up to MacGyver to get them out.
The rebel leader Rafael arrives, and Santina tells him about the prisoners. He checks Pete's ID and is well aware that the Phoenix Foundation has connections to the U.S. government, including the DXS. Santina isn't convinced that Enrique is a traitor, but Rafael notes that not everyone is strong enough to remain sworn to the cause. He goes to see the prisoners but doesn't believe Pete's denial. When Sister Clara refuses to tell him what Enrique said, Sanford orders them to a nearby levee. He gives Clara one more chance and when she refuses to talk, Rafael shoots Pete in the shoulder. He threatens to shoot again and Clara admits that Enrique told her about the bomb. She assures Rafael that she didn't tell anyone else.
As Rafael considers what to do next, MacGyver and Jack land nearby, disguised as arms dealers. They offer the missile launchers for sale and Santina tests one. Rafael agrees to buy and they go to the camp for a celebratory drink. While Jack and Rafael share a drink, MacGyver gets Santina to show him the camp. She notes that she doesn't like arms dealers, since they provided the weapons that lead to the deaths of her parents. MacGyver goes to freshen up and then slips into the tent where Pete and Clara are kept prisoner. He frees them and lures in a guard, and then knocks him out. Next MacGyver throws an oil lamp into the nearby ammo dump. The guards come running and Jack knocks out Rafael. They run to the plane and MacGyver pre-starts it. They get away but Santina's men open fire and damage the oil line.
Jack manages to land the plane twenty miles away on a small stream. They come to the end of the stream and rip open one of the landing pontoons. One of Santina's lookouts sees them lands in and radios Santina. She tells him that she and her men will be there in three hours, and then informs Rafael that the mountains are too high for Jack and MacGyver to radio the capital city to warn Montoya. Rafael insists on accompanying her and leading his men.
Clara tends to Pete's wound and tells MacGyver about the bomb. They have six hours until the peace talks begin and no way to call out. MacGyver and Jack go to work, melting down strips from life jackets and mixing it with rubber to form a patch. As they work, Clara tells MacGyver that Pete will die with hospitalization, and that Rafael shot Enrique, his chief of staff, when Enrique learned that Rafael was going to assassinate the President.
As they proceed cross country, Rafael begins to bully the men and worry about how the situation will affect him personally. Santina realizes his lack of commitment to the cause. When they get stuck in mud, a frustrated Rafael snaps at Santina's men and orders them to proceed on foot.
Jack and MacGyver finish the repairs and MacGyver assures Pete they'll be okay. Pete says he's honored to be MacGyver's friend and then passes out from blood loss. They load up the plane but realize they don't have enough stream to take off. MacGyver suggests anchoring the plane and running the engine full out until they have enough velocity, but Jack warns it won't be enough. He suggests needing a rocket to achieve takeoff speed and MacGyver improvises using the missile launchers.
Santina suggests to Rafael that they contact the fugitives on the radio and offer them the chance to surrender. Rafael refuses, insisting he want the glory of capturing them. Santina contacts MacGyver privately to offer him surrender. MacGyver refuses and warns her that Rafael is scheming for himself, not the revolution. He passes on the information from Clara that Rafael shot Enrique in the back to silence him, and she should be careful. Santina tries to advise Rafael to approach the fugitives with caution, but he accuses her of incompetence and threatens to relieve her of command if she doesn't obey him.
MacGyver fastens the missile launchers to the underside of the plane and rigs a firing device to trigger both items simultaneously. They then tie a rope from the plane to a log and prepare to depart. The rebels arrive and Rafael orders mortar fire. Santina's man misses with the first shot and Santina informs Rafael that was there last mortar rounds. She takes command again and leads her men toward the stream. Jack starts the plane and runs the engine to maximum, but MacGyver discovers Jack's slipknot is stuck. MacGyver climbs onto the pontoons and cuts the line. The plane lifts off, flying out of rifle range. When Rafael challenges Santina's disobedience, she has her men arrest him.
The plane clears the mountains, and Clara contacts the Presidential palace to notify Montoya's men about the bomb. Pete wakes up and wonders where MacGyver is, and Jack avoids telling him that MacGyver is still holding onto the bottom of the plane
Late, Jack and MacGyver meet with a recovered Pete at his office. Santina successfully completed the peace talks and convinced Montoya to run the first free election. Jack asks if Pete is doing better… and then gives him the bill for repairs. He quickly leaves while Pete asks MacGyver to never ask Jack for another favor again.