Pete's son and ex-wife Michael and Connie Thornton are working an archaeological dig in the Louisiana bayous. Michael still has issues with his father, who didn't show up for his high school graduation and cited work as an excuse. They're interrupted when masked and armed men capture them and then take video footage.
At the Phoenix Foundation, Pete receives the tape of his family being abducted. He shows it to MacGyver and explains that they were unable to find any clues in the tape or the message that came with it. The message instructs Pete to go to Sherman Parish, Louisiana. MacGyver immediately starts preparing to leave, even though Pete can't bring himself to ask.
Connie and Michael are being held at a cabin in the bayous. The head man, Frank Bonner, warns his assistant Boone not to underestimate Pete when he arrives. Bonner then goes into the cabin where Connie and Michael are being held and tells them he's an old friend of Pete's. He set up the grant that lured them to the bayous and explains that they're there as bait.
MacGyver gets to Louisiana three hours ahead of Pete, rents a motorcycle, and goes to the road where Pete was instructed to meet with the kidnappers. He's equipped with a receiver set to the frequency of the signal watch that Pete is wearing. When Pete arrives at the designated spot, Boone and his men Dunn and Corey pick up Pete in a SUV and drive him down the road. MacGyver first follows at a distance and then passes them. Up ahead, MacGyver spots an empty truck and figures the kidnappers will make a switch.
Boone and his men arrive and make the switch. Pete spots MacGyver in the bushes and stalls for time as they have him change into clothing they provide. He drops the signal watch and MacGyver manages to grab it, sneak under the new vehicle, and attach it to the underside. Boone and the others drive Pete to a dock and go past a local fisherman to load Pete on the boat. Corey takes the second vehicle and continues driving down the road.
MacGyver catches up to the second vehicle and realizes Pete is no longer in it. He backtracks and finds the dock. The fisherman, Obadiah Moss, initially denies seeing anything but after MacGyver displays his knowledge of fly-fishing, he warms up. Obadiah tells MacGyver that the men must have taken Pete to a cabin in the swamp, the only piece of dry land for miles. He directs MacGyver to look for a tire nailed on a post near the cabin. MacGyver rents Obadiah's boat and departs. As soon as he's gone, Obadiah uses a hidden walkie-talkie and tells Bonner that MacGyver's on his way.
Bonner goes to see Pete and his family and tells Connie and Michael that they used to work together. He plans to force Pete to tell the truth and leaves, but Pete has to admit he has no idea what Bonnier is talking about. He does explain to his family that Bonner was a former agent who was too violent. When Michael wonders what he's doing to rescue them, Pete admits he only brought one man.
MacGyver quickly realizes that Obadiah's attitude changed too easily, and that the supposedly handmade fishing flies on his hate were store-bought. He creates a dummy out of a discarded life jacket, a paddle, and a board, and ties it to the skiff's steering wheel. Bonner goes to tell Pete that they've spotted MacGyver and are going to kill him. Dunn and Corey spot the skiff and open fire with a LAW rocket, blowing it out of the water. Dunn reports in that MacGyver has been killed and goes back to the cabin. MacGyver, having followed the boat along the shoreline, puts a few hundred dollar bills in the life jacket and floats it toward Corey, then knocks him out from behind. He takes Corey's clothing and ties him up.
After Bonner has left, Pete assures Connie and Michael that MacGyver isn't that easy to kill. Michael, angry, insists they need to do something. When Bonner comes back in, Michael yells at him and Bonner beats him. He finally tells the Thorntons that his wife and son were killed, and Pete was responsible. He sets up a mock courtroom and puts Pete on trial, describing how they were in Yemen three years ago. Supposedly the area was secured and Bonner moved his wife and child there. Pete notes that a tribal war started up without warning and Bonner accuses him of escaping and leaving Bonner's wife and child behind.
Dressed as Corey, MacGyver gets close enough to Dunn to knock the henchman out. MacGyver then attaches a rope to the drive of a donkey engine, and splices fishing line in and hooks it to the ignition switch so he can yank on the rope from a distance and turn it on.
Pete testifies as to what really happened: Bonner embezzled the money they were supposed to use to buy intelligence on local tribes and then faked information of his own. Without the information to protect themselves, the agents were defenseless when the tribes attacked and Bonner's family was killed and Pete himself was wounded. Pete refuses to blame himself and accuses Bonner of killing his own family through his negligence. Bonner refuses to accept the facts and plans to kill Michael.
MacGyver ties a bar to the rope and then runs the bar through the slats on a window. He then creates rigs a gas can to explode using an oil-soaked rag. It explodes and MacGyver goes to the cabin. Bonner goes to investigate and MacGyver activates the engine, ripping the wall of the Thorntons' room off. They run into the woods but Connie trips. When Pete goes back to help her, Obadiah arrives in camouflage and takes them prisoner. Michael starts to go back for his parents but MacGyver stops him. Boone and Obadiah go to search for Michael and Bonner takes Pete and Connie back to the cabin.
MacGyver and Michael evade Boone and Obadiah and MacGyver comes up with a plan. He starts filling bamboo stalks with methane gas from the swamp and then sealing them with mud. As they work, MacGyver explains that Pete's work was classified and he couldn't say anything to his family. By the time the mission was declassified, Michael was no longer speaking to his father. Although Pete missed Michael's high school graduation due to his work, MacGyver promises that he'll be there for Michael's college graduation.
In the cabin, Bonner tells Pete that if they don't find Michael, he'll force Pete to watch his ex-wife die. After sunset, MacGyver approaches the cabin and knocks out Dunn. When he realizes they're under attack, Bonner takes Pete and Connie out of the cabin and has Boone shoot Connie. Pete tries to stop him and Bonner clubs him to the ground.
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. MacGyver and Michael arrive and throw the bamboo stalks. Boone tries to shoot one out of the air and it explodes, knocking him out. MacGyver throws another one at Obadiah but it's a dud. Using the stalk as a staff, MacGyver manages to knock Obadiah out. Pete goes after Bonner and knocks him to the ground. Michael grabs Bonner's gun and prepares to shoot his captor, but Pete and MacGyver remind him that he's not a killer.
Later, the Thorntons are enjoying a Cajun meal at MacGyver's apartment. Pete invites his son to a Lakers game, and Connie says they have a lot of catching up to do. Michael accepts, and MacGyver burns his blackened redfish and suggests they go out for cheeseburgers.