A woman general is being held at a beach house by foreign operatives and MacGyver is sent in to rescue her. He uses his Swiss Army knife to jimmy the patio door lock and get inside to the kitchen, then goes through the refrigerator to find something to create a distraction. He takes out a bag of carrots and a tray of ice, puts the ice in a plastic bag, and balances metal pots on a tray. He uses the ice as a counterweight and then turns on the toaster oven. Grabbing a bottle of vegetable oil, he coats the floor inside the kitchen door. After eating a carrot, he slips outside and waits for the pots to fall. The agents hear the noise, run into the kitchen, and trip. MacGyver goes in to get the general only to discover she's handcuffed rather than tied. He slides her outside onto the patio then stretches a garden hose across the exit. When the agents run outside, they trip and fall onto the beach below, and he grabs their guns and calls the police.
Next, MacGyver gets a code red priority to take out a Middle East dictator's nuclear plant. He returns home and notices the doormat is disturbed. He turns on a hidden ultraviolet life that reveals someone stood there. Going inside, he finds his government contact, Barney, waiting for him. Barney offers his congratulations and warns that he was ID'd during the mission and the dictator has hired a hitman, Axminster. He warns that Axminster will take out the entire block to get him and offers him protection, but MacGyver says he has a trip he wants to take. He refuses to tell Barney where he's going and insists that it's personal.
MacGyver takes a bus to Colorado and goes to visit his grandfather, which he hasn't seen since he was 10. Meanwhile, MacGyver's grandfather Harry Jackson calls his grandson and gets his answering machine. He leaves a message telling MacGyver not to come. Axminster's man has the phone tapped and prepares to trace the phone number that Harry leaves.
MacGyver gets off the bus and finds Harry waiting for him. Harry isn't too thrilled to see him and grudgingly takes him up to the farm.
Axminster locates Harry by the phone number and takes his men up to Colorado.
Harry and MacGyver arrive at Harry's rustic cabin and Harry mentions his wife dying. MacGyver wonders why Harry left without a goodbye shortly after his wife and MacGyver's father died. Harry explains he took a job in Alaska and sent money back, but MacGyver notes it wasn't enough.
Axminster and his men arrive in jeeps and head toward Harry's cabin, heavily armed. He tells his men that he wants MacGyver dead. Meanwhile, MacGyver and his grandfather enjoy breakfast and Harry wants to know why his grandson is there. MacGyver admits he ran out of reasons to put off visiting, and Harry says he hasn't thought of family in years. MacGyver notices a duck whistle he made for Harry when he was ten. Axminster and his men surround the cabin and burst in... and discover that MacGyver and Harry have left to go fishing. They're out on a lake on a boat and Harry notes he plans on dying there. MacGyver talks about how he and his mother missed him most around the holidays and Harry tells him to drop it. MacGyver starts to reel in a fish... and one of Axminster's men finds them and opens fire. They dive into the water, swim to shore, and run into the woods. MacGyver sticks two hollow reeds into a piece of bark and floats it across the lake to draw Axminster's attention so they can buy some time to escape.
As they flee, MacGyver spots a plant with a paralytic sap and Harry extracts the sap while MacGyver makes a crude blowgun out of hollow reeds and wood slivers. However, he warns that he'll have to hit them right in the neck. They leave tracks to draw off two of the men and MacGyver shoots one of them in the neck. He only hits the other one in the arm but Harry hits the man over the head with a branch to knock him out. As they run, Harry demands to know why they're after MacGyver. He explains that he works for the government. Meanwhile, Axminster abandons his two downed men and keeps going.
As they go down the road, Harry tells them there's a small town, Evermore, nearby in the desert that should have a phone line. As they run, MacGyver spots a sharp piece of flint and takes it along. He climbs up a tree and spots the jeeps, and figures they've got a little time. He has Harry create a decoy out of a jacket stuffed with weeds and starts cutting a heavy branch with the rock edge. When one of the jeeps drives by, Harry tosses out the dummy and MacGyver jumps on the branch, dropping it on the men and forcing them off the road. However, the jeep is ruined and Axminster and his three remaining men close in on the jeep. MacGyver stops to gather pine cones and cover them with pitch, then buries them where the jeep has to pass. When it stops to shoot at them, they throw more of the pinecones under the jeep to try and set off the "mine." Axminster wings Harry with one shot, but MacGyver sets the mine on fire, blowing up the jeep. Axminster and his three remaining men continue the chase on foot while Harry starts to falter. They get to the town... only to discover that it's been abandoned for years. Harry collapses from blood loss and falls into his grandson's arms.
Night falls and Harry tries to make Harry comfortable and creates a crude antibiotic. Harry admits that he avoided MacGyver all these years because he reminded him of his daughter after she died. He kept moving so he wouldn't have to remember, but admits that he missed MacGyver. They hug and then MacGyver starts looking for items to fight with. The next morning, Axminster takes up the trail and closes in. MacGyver finds some grain dust to use as a bomb, filtering it into a room. Harry rigs a fishing string to a curtain to lure them in, then gets some pine nuts to throw into a fire to simulate gun shots..
Axminster and his men arrive and MacGyver pours some grain into a room. Harry twitches the curtain and when two of the men approach the door, MacGyver tosses in a match and the explosion takes them out. Harry starts a fire and tosses the pinenuts in, suckering in a gunman so Harry can knock him out with a two-by-four. Axminster climbs to high ground on a balcony and jumps on MacGyver when he passes underneath. When Axminster goes for his gun, Harry attacks him and MacGyver gets back his second wind and gets him into position under the weakened balcony. MacGyver leaps for the post and brings down the structure on Axminster, knocking him out.
Later, MacGyver prepares to leave but says he'll be back and Harry says he'll be looking forward to it. The two men hug and MacGyver tells him to catch a trout for him.