MacGyver drives out to Dead Horse State Park to follow a pair of mating Golden Eagles and find their nest, as part of a Phoenix Foundation program. He's to make sure the eggs are protected from natural hazards as well as men. MacGyver takes a hang glider up into the mountains to follow the eagles. He tracks them to an inaccessible peak, assembles the hang glider, and flies after them. He copies the eagles' flight path so they'll be comfortable enough around him to go back to their nest. On the ground below, a young boy, Darin Cooper, is out with his dog and spots MacGyver while watching the eagles. MacGyver flies by him and waves.
Two excursion guides, Ghant and Curry, are flying a hunter, Nistrum, into the area by helicopter so he can bag some trophies. Nistrum starts shooting at the eagles and MacGyver and Darin both spot him. Nistrum misses with his rifle and switches to a crossbow. He wings one of the eagles then goes after the other one. MacGyver blinds the pilot, Ghant, with a mirror and the helicopter hits the other eagle with the skid. The three men fly away as the second eagle crashes to the ground in shock. MacGyver doesn't have enough lift to get to it on the mountain so he goes to help Darin with the first eagle. MacGyver manages to snag it with his coat and Darin takes them to his family cabin. His mother Susan is trying to start her truck without success when Darin and MacGyver arrive. They take the eagle to the shed and Darin tries to help, but Susan warns him repeatedly to be careful. MacGyver has her hold the eagle while he wraps and splints the broken wing. As they work, Susan explains the cabin belongs to her father and she brought Darin out there to fix some things between her and her son. Once they're done, Susan calls out to Darin and then points out the rock where Darin goes after they've had an argument.
Back at the excursion hangar, Ghant and Curry worry that MacGyver will go to the authorities because they shot an endangered species. Nistrum tells them to find something on MacGyver to bribe or blackmail with him with. Once Nistrum goes, Ghant worries that since he's an escaped murderer, any hint of a crime could bring the authorities down on him.
MacGyver tells Darin that the eagle is recovering and Darin talks about everything he knows about Golden Eagles. MacGyver assures him the eagles will be okay and then says that Susan is worried about him. Darin doesn't like the fact she's so overprotective. MacGyver suggests that he try and talk to his mother. That night, Susan checks in as Darin watches over the eagle. MacGyver returns with his hang glider and offers to give Darin a flight, but Darin insists that Susan would never let him. He begs Susan to let him sleep with the eagle but she refuses. Darin stalks off and Susan worries that MacGyver let Darin use his knife. She gives it back and MacGyver apologizes for not asking first.
The next morning, MacGyver takes some sugar cubes for the second eagle on the mountain and then goes to see the wounded bird in the shed. He improvises mountain climbing equipment from what's in the shed while Susan comes in. She warns that the eagle is atop a sheer rock face but MacGyver insists on going. Susan gives him her father's red hat so they can spot him.
Ghant and Curry find MacGyver's jeep and learn his name from the registration papers. Curry just wants to talk but Ghant is eager to kill him.
MacGyver starts scaling the mountain while Ghant and Curry spot his hang glider at Susan's cabin. As they get back in their truck, they drop one of their crossbow bolts. Meanwhile, Darin watches MacGyver with his binoculars as he ascends one piton at a time. Ghant and Curry hide their truck and walk to the cabin. They ask about the hang glider and then claim a tree at the entrance to the park crushed his jeep. They spot him on the mountain, while Darin notices that Ghant is carrying a crossbow like the one that was used to shoot the eagle.
As MacGyver climbs beneath an overhang, he loses one of his tent stake pitons and then another hook goes, slamming him into the rock wall. Once he gains his second wind, MacGyver swings back to his cable. Meanwhile, Ghant worries that Darin is watching him suspiciously.
MacGyver continues his ascent, following the second eagle's cries. He finally gets to the bird, snares it with his jacket, and takes it into a cave to wait out the approaching storm. Down below, Susan puts Darin to bed while Ghant and Curry wait for him. When she starts to call the park ranger to tell him MacGyver is trapped, Ghant shows her that he severed the radio cord.
Throughout the night, MacGyver feeds sugar water to the eagle. In the morning, MacGyver digs himself out of the cave and puts the eagle in his pack. He starts down the mountain and finally gets to the bottom. As he heads down the road, he spots the crossbow quarrel that Ghant dropped early and recognizes it. He spots Ghant in the cabin window and stashes the eagle, then sneaks through the woods. Inside, Darin remembers that Ghant was the man flying the helicopter and Ghant overhears him. He prepares to kill Darin and Susan with his crossbow, then wait for MacGyver to return. Curry balks but Ghant reminds him that they used the take from his robbery to start their excursion outfit. Meanwhile, MacGyver sets up a grindstone and turns on a tank of propane. He plans to hit the grindstone with ball bearings and ignite the gas. MacGyver gets the first eagle out and then make a slingshot out of a bicycle's handles and an old inner tube, with the ball bearings as ammo.
When Ghant starts to hit on Susan, Darin hits him and then runs outside. Curry grabs him and brings him back inside, and MacGyver fires a rock onto the roof. Ghant comes out to investigate and MacGyver tries to hit the grindstone with ball bearings. All he does is break the window. Ghant fires at the grindstone and hits it, setting off the gas and blowing up the shed. The explosion stuns the felon. Curry comes running out to investigate and picks up the crossbow. MacGyver was also apparently stunned and Curry has no choice but to shoot him. However, MacGyver kicks a board up and knocks him out.
The police take Ghant and Curry away and MacGyver assures Susan that the authorities have Nistrum's name. Darin checks on the first eagle and discovers that it's dead. MacGyver assures him that they can still find the nest. He lets the second eagle go and then follows it on the hang glider. As he leaves, Susan admits to Darin that she's proud of how he handled things. Meanwhile, MacGyver follows the eagle to nearby Monument Park and the tallest butte in the park. MacGyver manages to land on the butte, packs away the eagles' eggs, and flies back to the cabin.
Back at the cabin, Susan gives Darin his grandfather's knife. MacGyver returns and makes a crude incubator. That night, the eggs hatch as everyone watches. And later, MacGyver takes Darin hang gliding to follow the eagle.