As part of a Phoenix Foundation to protect endangered Golden Eagles, MacGyver goes to Dead Horse State Park to use a hang glider to locate the eagles' nest and make sure that their eggs are protected from predators, both human and animal. He assembles a hang glider and matches their flight path to get them comfortable enough with him to lead him back to their nest. As he flies overhead, MacGyver spots a young boy, Darin Cooper, out with his dog Fred watching the eagles.
Two excursion guides, Ghant and Curry, are flying a rich hunter, Nistrum, by helicopter. He's already killed a ram but wants something unique to boast to his friends about. He spots the eagles and opens fire with his rifle. He switches to a crossbow and hits one of the eagles in the wing. MacGyver blinds the pilot, Ghant, with a pocket mirror, and the helicopter strikes the second eagle. As the second eagle glides to a nearby mountain in shock, Ghant flies back to his base.
MacGyver doesn't have enough lift to get to the second eagle so he flies down to help the first eagle. Darin is there and helps MacGyver restrain it. They take it back to the cabin where Darin is staying with his mother Susan. They take the eagle to the shed, and Darin tries to help MacGyver, who asks the boy to help using his Swiss Army knife. His mother keeps warning him to be careful and limiting what he can do. Angry, Darin leaves. MacGyver manages to split the broken wing and remove the crossbow quarrel. Susan explains that the cabin belongs to her father and she and Darin came there to work things out between her and her son. Once they're done, Susan shows MacGyver where Darin goes after they've had an argument.
Back at their office, Ghant and Curry worry about what will happen if MacGyver goes to the authorities and tells them they were responsible for an attack on an endangered species. Nistrum tells them to find a way to bribe or blackmail MacGyver to ensure his silence. He leaves and Ghant worries if the authorities find him, they'll identify him as an escaped death row prisoner.
MacGyver goes to see Darin and tells him the eagle is doing better. Darin talks about the eagles and how his dad, divorced from Susan, sends him books on eagles. He hates that his mother is so overprotective, and MacGyver suggests he try and tell her how he feels.
That night, Susan checks on the eagle and Darin, who is watching over it in the shed. MacGyver offers to give Darin a hang glider ride but Darin warns that his mother would never allow it. He asks his mother to let him sleep out in the shed with the eagle but she refuses to let him and orders him to bed. She gives MacGyver back his knife, and he apologizes for letting Darin use it without asking her permission. As he waits for dawn, MacGyver hears the second eagle crying out from the mountain.
The next morning, MacGyver prepares to climb the mountain. He packs sugar cubes to make sugar water, an ink pen to make a feeder, and tent pegs and dog leash clips as makeshift climbing equipment. Susan gives him her father's red hat so she and Darin can follow his ascent up the mountain.
Ghant and Curry look for MacGyver and find his jeep. They get his name from the registration papers and Curry insists they just want to talk. Ghant figures it'll be safer to kill MacGyver, and he has nothing to lose by another murder. Watching from a distance, they spot MacGyver's hang glide at Susan's cabin. They go to move their truck, dropping one of their crossbow quarrels on the road. They approach the cabin and claim that a tree crushed MacGyver's jeep. They watch along with Darin as MacGyver scales the mountain, and the boy notices they have a crossbow like the one the eagle was shot with.
MacGyver manages to get to the top of the mountain, following the eagle's cries. As a snowstorm moves in, MacGyver gets the bird into a cave and nurses it with sugar water. Dow below, Ghant and Curry wait at the cabin. However, when she tries to call the park ranger to tell him about MacGyver's predicament, Ghant reveals he's destroyed her radio.
The next morning, MacGyver digs himself out of the cave and heads back down the mountain, carrying the eagle in his pack. He makes the trip in record time but as he comes down the road toward the cabin, he spots the crossbow quarrel on the road. Recognizing it as the same one he pulled from the eagle, he sneaks up to the cabin and spots Ghant. After hiding the eagle, MacGyver goes to the shed. Meanwhile, Darin finally remembers that he saw Ghant flying the helicopter. Ghant ignores Curry's objections and prepares to eliminate the boy and his mother.
MacGyver sets up an old grindstone by the window to the shed and then opens the valve on a tank of propane gas. He then takes some ball bearings, a bicycle, and an inner tube, and takes them out along with the wounded eagle. He then sets up the bicycle handles with the inner tube to make a slingshot and prepares to fire the ball bearings at the grindstone and create a spark to ignite the gas.
Inside the house, Darin hits Ghant and starts to run outside. Curry grabs him and pulls him back inside, so MacGyver throws a rock onto the roof to draw Ghant out. When the escaped prisoner comes out, armed with the crossbow, MacGyver fires ball bearings at the grindstone. He misses and breaks the window, and Ghant fires at the sound. His shot ignites the propane, the gas ignites, and the shed explodes. Ghant is stunned and Curry comes out to find an unconscious MacGyver lying a short distance away. Curry reluctantly moves over to kill him but MacGyver is playing possum. He kicks a board into Curry and then punches him unconscious.
As the police take the two guides away, MacGyver makes sure that they have Nistrum's name and the hunter will be properly dealt with. However, the first eagle has died of its wound. MacGyver assures him that as long as they can find the nest, they can save the family. He releases the second eagle and follows it by hang glider, while Susan tells Darin that she's proud of him.
MacGyver follows the remaining eagle to a towering butte in nearby Monument Park. He manages to land the hang glider and recover the eggs. Back at the cabin, MacGyver makes an incubator out of chair padding and vegetable. As they wait for the eggs to hatch, Susan gives Darin his grandfather's Swiss Army knife as a token of her trust for him. The next morning, the eggs hatch, and MacGyver gives Darin a hang gliding flight up with the eagle.