Connie Thornton and her son Michael are working at an archaeological dig in Louisiana. As they work, they discuss how Connie's husband Pete didn't show up for Michael's graduation and always used work as an excuse. Masked men burst into the camp, capture them, and then take video of them.
The men send the videotape to Pete, who shows it to MacGyver. There are no clues in the message or the tape, and the kidnappers want Pete to fly to Sherman's Parish, Louisiana. MacGyver insists on going and Pete notes he can't ask him to help. MacGyver tells him he doesn't have to.
At the abductors' cabin in the woods, their leader, Frank Bonner, tells his assistant Boone that Pete will arrive in the morning and warns him not to underestimate their opponent. Bonner then talks to Connie and Michael and introduces himself as an old friend of Pete's. He explains that he arranged for the grant that brought them down there, so he could use them as bait.
MacGyver gets into Louisiana three hours early, rents a bike and a map, and gets into the swamps. He checks out the road where Pete is supposed to go to meet the kidnappers. Pete has a watch that emits a radio signal and MacGyver has a receiver. The cab brings Pete to the designated spot and lets him out. A car arrives and Bonner's men order him in. Pete gets in and activates his watch, and MacGyver follows them. He passes by them and then spots an empty truck on the road ahead. MacGyver figures the kidnappers are planning a vehicle switch and waits for them to arrive. The abductors arrive and have Pete remove his clothing and jewelry and then clothing of their choosing. MacGyver crawls under the original car and then grabs the watch when Pete drops it. Pete asks for a minute to dress in private and the kidnappers agree. MacGyver crawls back into the brush and then attaches the radio to the underside of the second vehicle. Once Pete has finished changing, Boone drives Pete through the swamps while MacGyver follows the radio signal. They take Pete to a dock past a fisherman and load him onto a boat, then take off into the swamps.
Another of Bonner's men drives back along the road in the truck. MacGyver realizes no one is in it and has no choice but to time his ride to determine where they were let off. He finds the dock and talks to the fisherman, Obadiah Moss. Obadiah says he hasn't seen anything and MacGyver discusses fly-fishing. After Obadiah warms up to MacGyver as a fellow fisherman, he tells them that Pete and Bonner's men headed up into the swamp. Obadiah figures there's only one place they could have gone, a piece of dry land up the river. MacGyver thanks him and Obadiah gives specific directions, and then warns that Pete didn't look happy. MacGyver rents Obadiah's boat despite his warning it's in poor shape. However, once he's gone, Obadiah uses a secret radio to call Bonner and tell him MacGyver’s on his way and when he'll arrive.
As he heads up river, MacGyver realizes that Obadiah's attitude changed too quickly and he knew too much, and his supposed self-tied fishing flies were store-bought. Meanwhile, Pete is taken to Bonner's cabin and reunited with his wife and sun. Bonner introduces himself and Pete explains that they worked together. He wants Pete tell the truth and then promises he'll demand payment in full. Once he's gone, Pete admits he has no idea what Bonner is talking about. He apologizes to Connie and explains Bonner was a top agent but enjoyed violence too much. Michael isn't happy that Pete has only brought one man.
MacGyver arrives at Obadiah's designated location and creates a dummy, then sends the motorboat on ahead. Bonner informs Pete that he knows about MacGyver and then calls his man Dunn, who is preparing to open fire. Dunn spots the boat and the dummy and opens fire with a LAW rocket. The boat is destroyed and Dunn informs Bonner that MacGyver has been eliminated, then puts his partner Corey on watch. Meanwhile, MacGyver takes the life jacket from the dummy he made and puts a few hundred dollar bills on it. He floats it down river and Corey spots it. When he goes to get it, MacGyver comes up behind him and knocks him out, then takes his clothing and ties him up.
Once Bonner locks up the Thorntons again, Pete assures his family that MacGyver is unlikely to have died. Michael doesn't believe him and insists they need to do something. Bonner comes in and beats Michael when he yells at him. Connie demands to know what's going on and Bonner says that Pete killed Bonner's wife and son. He then sets up a mock courtroom and begins his presentation. He explains that he was in Yemen three years ago with Pete and moved his wife and child there after Pete said it was under control. Pete reminds him that he knows what went wrong: a tribal war started up. Bonner accuses him of running out on Bonner's wife and child.
MacGyver enters the camp and gets close enough to Dunn to knock him out. He then attaches a rope to a donkey engine but needs a timing device. Using some fishing line, he sets up the engine so he can activate it from a distance.
Pete explains that Bonner was in the field, and Bonner claims he sent his family to Pete for safekeeping. Pete points out that Bonner had $800,000 to buy information to secure their safety, but he embezzled the money and provided fake intelligence information. Pete was hit in the same attack that killed Bonner's family and refuses to accept the guilt that Bonner is blaming himself over. Bonner doesn't believe it and insists there'll be an execution, but he wants Pete to see his son dead the same way that Bonner did.
MacGyver attaches the rope to a bar and threads it through the bars on a window at the cabin. He then sets up a crude Molotov cocktail and gets back to the cabin. As Bonner prepares to shoot Michael, the gas can explodes. Boone locks up the Thorntons while Bonner goes to investigate. MacGyver activates the engine, ripping the window out of the wall and freeing Pete and his family. They run into the woods but Pete and Connie fall behind and Obadiah arrives. Michael starts to go after them but MacGyver finds him and holds him back. He warns the boy they have no choice but to escape and come back later. Bonner tells Obadiah and Boone to find Michael and escorts Connie and Pete back to the cabin.
MacGyver and Michael evade their pursuers and Michael wants to know what they're going to do. MacGyver starts making explosives out of methane-filled bamboo stalks. Meanwhile, Bonner finds Dunn and puts him on first watch. As they work, Michael admits that Pete was never close to him and MacGyver points out that at least Pete tried. He notes that Pete's work were classified and he couldn't say anything to Michael even though he wanted to. When the mission was declassified, Michael wasn't talking to Pete any more. MacGyver assures him that when he graduates from college, Pete will be there.
Pete warns Bonner that MacGyver has escaped but Bonner warns if they don't find him by morning, Connie will die first and then Pete.
MacGyver approaches the cabin and distracts Dunn with a thrown rock, and then renders him unconscious. Bonner forces Connie and Pete out of the cabin and then orders Boone to shoot Connie. When Pete tries to interfere, Bonner knocks him down. However, MacGyver and Michael throw the bamboo explosives. Boone shoots one and it explodes, knocking him out. MacGyver throws another one at Obadiah but it doesn't go off. MacGyver leaps on Obadiah and manages to disarm him using the bamboo as a staff. Pete trips Bonner and then takes him down. Michael grabs Bonner's gun and prepares to shoot him. Pete points out that he's not a killer and MacGyver backs him up, and Michael lowers the gun.
Later at MacGyver's apartment, MacGyver is making a Cajun meal for the Thorntons and Pete invites Michael to a Lakers game. Michael accepts and Connie says they have a lot to catch up on. Pete admits he's proud of her. MacGyver serves his blackened redfish and burns it, and suggests they go out for cheeseburgers.