MacGyver is sent to rescue a woman general captured by enemy agents who are holding her at a beach house. MacGyver slips into the kitchen and creates a distraction by balancing a bag of ice on a tray holding pots and pans. He turns on the toaster oven by the ice, and then pours cooking oil on the tiled floor. When the ice melts and the pans fall, the agents run in and slip and MacGyver goes for the general. However, she's handcuffed to the chair so he pulls her outside and pulls a garden hose across the doorway. When they run outside, they trip and fall into the sand below and MacGyver quickly disarms them and calls the authorities.
MacGyver is then off to the Middle East to infiltrate a dictator's nuclear plant and destroy the place with explosives. Returning home, he discovers that someone has entered his apartment. Going inside, he finds his government contact Barney waiting for him. Barney informs him that he was identified during the mission and the dictator has handled Axminster, a brutal hit man who killed dozens while taking out a target in South America. MacGyver refuses Barney's offer of protection and says that he has a personal trip that it's time to go on.
MacGyver takes a bus to Colorado to visit his grandfather Harry Jackson. He's unaware that Harry is trying to call to tell him to stay away. Harry leaves a message on MacGyver's answering machine telling him to call back to the local general store. Axminster is tapping MacGyver's phone lines, has his man locate where the number is, and takes his team of mercenaries to Colorado.
Harry greets MacGyver at the bus stop and clearly isn't thrilled to have him there. He takes him up to his cabin and MacGyver wonders why he left his daughter and grandson after his wife died. Harry explains that he thought they'd be better off without him, so he got a job in Alaska and sent money back. MacGyver says it wasn't enough.
The next morning the two men eat breakfast and prepare to go fishing. Harry asks why MacGyver is really there and MacGyver admits he simply ran out of reasons to stay away. Harry claims he hasn't thought of his family for years. Axminster and his men arrive by jeep and burst into the cabin… to discover they're already gone. On the pond, Harry and MacGyver are fishing and MacGyver tries to bring up Harry abandoning them. Harry refuses to talk about it and tells his grandson to drop it. MacGyver catches a fish, but one of Axminster's men finds them and opens fire. They dive over the side of the boat and swim to shore. Once on solid land, MacGyver puts two hollow reeds into a piece of bark and pushes it across the pond so Axminster will think they're trying to get away underwater. The ruse works long enough for MacGyver and Harry to get further away.
MacGyver spots a plant with a paralytic sap and makes a crude blowgun. They poison makeshift darts with the sap, but it needs to go into the neck to take effect. They draw off two of the men to a creek and MacGyver hits one of them in the neck with a dart. He only wings the other man, but Harry steps up and knocks the man unconscious with a heavy branch. Bemused that MacGyver took his stories of Indian woodcraft seriously, Harry asks what he does for a living. His grandson explains that he works for freedom and liberty.
They keep going with Axminster and his remaining men in pursuit. Harry says there's a small town up ahead and they can call for help from there. One of the jeeps closes in and MacGyver has Harry stuff a jacket with branches to make a jacket while he cuts off a heavy branch with a crude stone blade. When the jeep drives by, Harry tosses out the dummy and the men stop long enough for MacGyver to drop the branch on them. They go off the road, damaging the jeep and making it undrivable. MacGyver and Harry head for the town while Axminster arrives in the last jeep.
Deciding to make a stand, MacGyver gathers pinecones and covers them with pitch from a tree. They coat the pinecones with the pitch and bury several of them at a narrow spot in the road. When Axminster drives through, they throw a burning pinecone to draw his attention and have him stop over the buried pinecones. The hitman and his mercenaries return fire and Harry is grazed in the side. MacGyver manages to throw another burning pinecone and ignite his makeshift mine, destroying the jeep. MacGyver helps the injured Harry get to the town, only to discover that it's been abandoned in the several years since Harry last visited.
That night, they take refuge inside and MacGyver makes a crude antibiotic out of iron pyrite and clay. Harry finally admits that he's avoided his grandson for the last 18 years because he couldn't handle having him around after MacGyver's mother, Harry's daughter, died. He's kept moving for years but still misses MacGyver. They hug and then MacGyver starts putting together a plan. He finds some grain dust and starts pouring it into a building through the ceiling. Harry, feeling better and with a few ideas of his own, rigs a fishing line to the building's curtain so he can twitch it from outside. He also explains to his grandson that he has some pine nuts and will throw them into a fire to simulate gun shots. Finally, MacGyver finds a saw and cuts most of the way through a support pillar for a second-story balcony.
Axminster and his three remaining mercenaries arrive. As Harry pounds on a pipe next to the building and twitches the curtain, MacGyver pours floating grain in through a hole in the top. When two of the mercenaries investigate, MacGyver tosses in a match and the resulting explosion knocks them out. They split up and Harry tosses some pine nuts into a fire. Another gunman shoots back only to discover he's been tricked, but Harry knocks him out with a board. Now that they outnumber Axminster, they go looking for the hitman. He drops on MacGyver from above and knocks him to the ground. Axminster prepares to shoot but Harry tackles him, giving MacGyver enough time to recover. He shoves Axminster below the balcony then dives for the weakened support, bringing down the balcony on top of the hitman.
Later, MacGyver is leaving on the bus and promises Harry that he'll be back. Harry says that he'll be looking forward to seeing him again.