The Phoenix Foundation "pays" MacGyver with an entry in a hot air balloon in the Alps. He goes up with a new female friend, Heidi, and they drink champagne together. Nearby, an American pilot in an experimental GX-1 stealth fight is evading Russian MIG fighters. The pilot calls in to base to give his coordinates and then tries to climb out of range of the enemy fighters. He succeeds but not before they shoot up the fuselage. He bails out as a wing blows off the plane and it plummets to the ground below.
MacGyver lands his balloon and Pete arrives to tell him the fighter has gone missing and they need his help. The Air Force can't track the plane and they need MacGyver to go in on foot. As MacGyver agrees and says goodbye to Heidi, he discovers that Pete has brought Nikki Carpenter along for the mission. They argue about their respective approaches and Pete interrupts to tell them they don't have a choice. Much to their chagrin, they discover they'll be going in as a married couple. Pete tells them that once they're over the border and at the resort, they can split up and do whatever they want.
The trio goes to a nearby hotel and reviews the recording of the pilot's last words. Pete warns that the Air Force is presuming the pilot died, but the transmitted coordinates narrow down the search area. Pete warns them that the Russians are also looking for the heat-suppression system. They have a psychic working for them: Starkoss. Pete shows MacGyver and Nikki a smuggled tape that demonstrates Starkoss' supposed psychic abilities. He explains that due to his abilities, the Russian government gives Starkoss every amenity, and warns that American Intelligence believe that Starkoss is authentic. MacGyver is skeptical of any kind of paranormal ability but Nikki is a bit more accepting.
In Moscow, Colonel Markov watches as Starkoss examines photos of the GX-1 crash. The psychic relives the pilots last moments in the plane and then realizes that his government deliberately shot down the plane. Markov insists that the pilot refused to surrender. Starkoss uses a map to indicate where he believes the GX-1 is located.
MacGyver and Nikki arrive at Aspenhaus in East Germany. MacGyver has managed to talk them past the border guards. Nikki makes snide comments about MacGyver's lady friend, Heidi. She flirts with Helmut, the spa attendant who greets them. MacGyver, disgusted, takes off in the car and heads for the mountains. Nikki goes into the resort and sports Markov and Starkoss leaving. She goes after MacGyver to warn him.
MacGyver has left the car and is hiking into the mountains. He spots the helicopter that Markov is using to coordinate the search. Nikki finds his car and goes up into the mountains after him. She stumbles through a stream and finds a farmer. Nikki manages to buy his horse despite the fact he doesn't speak English.
MacGyver camps for the night and hears someone approaching. He hides as Nikki stumbles into the camp, cold and wet. MacGyver comes out of hiding and Nikki explains that her horse through her into a stream and she's been walking to catch up with him. He gives her some of his own dry clothing and she tells him that she came to warn him about Starkoss. MacGyver thanks her and then points out that he only has one sleeping bag. Nikki refuses to share it with him and sleeps on the ground. The next morning, Nikki warms herself by the fire and sarcastically thanks MacGyver for acting like a gentleman.
The pair continues on foot and come to an abandoned mine. Markov and his men are already there. Starkoss has led them to the dead pilot, hanging in a tree by his parachute. Starkoss dons the pilot's glove and gets a psychic hint of where the GX-1 crashed. Markov tells his men to leave the pilot where they found him and continue on. As MacGyver watches through binoculars, Starkoss turns and looks directly at him.
Once the Russians move on, MacGyver cuts down the pilot. Nikki examines the pilot's wallet and finds a note from Starkoss telling them to follow. They both wonder why Starkoss is seemingly helping them and not telling his superiors everything he knows. Meanwhile, Starkoss leads the Russian soldiers to the GX-1. He faints and tells Markov he needs time to replenish his energy. Markov secures the area and calls in the helicopter to airlift a bulldozer in. MacGyver and Nikki arrive and MacGyver starts preparing explosives to blow up the pieces of the GX-1. Starkoss confronts them and explains that he wants to defect to the U.S. He knows all about them and claims that Nikki will save MacGyver's life. MacGyver agrees to help him but says that he'll have to destroy the plane first.
Starkoss goes back to the Russians and waits for the explosion so he can escape. MacGyver has Nikki stay behind while he slips into the crash site to attach the explosives to the plane pieces. The Russians spot him as he climbs up a hill and one of them prepares to open fire. Nikki clubs him unconscious, saving MacGyver's life just as Starkoss predicted. Markov's men shoot and MacGyver loses his grip, tumbling down the hill. He leaps over a cliff as the explosives go off. Markov, seeing his jump, assumes that he's dead. Starkoss escapes and gets to Nikki, telling her they have to get away.
Nikki and Starkoss return to the abandoned mine. MacGyver meets them there and they realize that with the Russian helicopter flying patrol, they have no chance to escape. They calculate that it will have to refuel in the morning. Meanwhile, MacGyver comes up with a plan. He tells Nikki to find all the fabric she can while he and Starkoss take apart the stovepipes. As they work, Starkoss grabs MacGvyer's hand and then tells him it wasn't his fault that he missed his mother's funeral, and his mother forgives him. MacGyver is taken aback but figures that Starkoss has been reading his personnel files. Starkoss explains that he's an authentic psychic but his abilities made him a freak. As Nikki returns, MacGyver tells Starkoss that they have to finish their work.
The next morning, the helicopter departs after running low on fuel. Markov realizes the fugitives must be at the mine and orders his men to close in. Meanwhile, MacGyver has made glue and is soaking all the fabric in it. He then dumps out the inside of a refrigerator casing and hook up tanks of acetylene gas. Finally, MacGyver gives the pilot's reserve parachute to Nikki just in case his plan doesn't work.
Markov and his men arrive as MacGyver, Starkoss, and Nikki escape in MacGyver's creation: a hot-air balloon lifted by burning acetylene gas, with the refrigerator casing as a gondola. It rises out of rifle range before Markov can bring it down. Nikki, overwhelmed with enthusiasm at their escape, kisses MacGyver. However, they run out of acetylene gas and sink toward the mountain. MacGyver has no choice but to lighten the load by having Nikki jump. She swears revenge on him as she parachutes safely to the ground below and the hot air balloon clears the mountain.
MacGyver and Starkoss land just over the nearby border. Starkoss realizes that American Intelligence will treat him as a freak just like the Russian government did. He says goodbye to MacGyver and starts walking down the road to find a life for himself. Nikki arrives, complaining, but pauses when she realizes that Starkoss is going off on his own. He waves to them as he enters the forest and slips out of sight.