MacGyver is at his home and scheduled to meet with Frank Bennett. The Federal Marshal, Wiley, has asked MacGyver to set up Frank for witness relocation after Frank testifies against the mob. Frank is reluctant to testify. MacGyver goes inside to call the missing Wiley, and two men abduct Frank into a car and drive away. MacGyver hotwires Frank's car and discretely follows them. The men tell Frank that his brother Joey wants to see him and take Frank to a lumberyard. MacGyver sneaks over the fence and watches as Frank's brother Joey Bennett and his Uncle Vincent arrive in their own car. Once they go inside, MacGyver unscrews the bolts on the two cars and then goes in after them.
Joey sends his men away so he can talk to his brother Frank in private. Frank insists he doesn't want anything to do with the family business anymore and isn't planning on testifying. Joey informs him that their mother is ill and fading in and out, and then asks why Frank has been talking with the Federal Marshals. Frank tells him that he's learned that Joey is handling drugs—drugs that are killing kids. He promises not to testify if Joey will get out of the drug business, but Joey insists that he needs the money to make payroll. Frank says he's ashamed of him, and Joey slaps him. Joey prepares to kill him, and Frank tells him to do it himself as a courtesy. As Joey prepares to shoot, MacGyver rigs a table saw and a shop vac to shoot lumber and sawdust into the air. While Joey and his men are distracted, MacGyver gets Frank out and over the fence. When Joey and his men try to pursue, the cars fall off their wheels.
Back at MacGyver's apartment, Frank admits he still isn't sure. Wiley arrives and convinces Frank that testifying is the right thing. Frank wants to see his mother Katarina first, but Wiley and MacGyver agree that it would give Joey the perfect opportunity to kill him. Frank gets MacGyver to promise that he'll explain things to Katarina. Wiley takes Frank to the Federal courthouse, and MacGyver visits Katarina and tells her that Frank will be testifying against Joey. Katarina understands and tells MacGyver that she's dying and needs to see Frank one last time. MacGyver reluctantly agrees, but as he leaves, he runs into Joey at the hall. Joey threatens MacGyver but refuses to make a scene in the hospital, and tells him to warn Frank that he'll be gunning for him.
At the Federal courthouse, Frank finishes testifying to Wiley and his men. MacGyver arrives and talks to Wiley outside, but the Federal Marshal refuses to take the risk of exposing Frank at the hospital. MacGyver is angry, insisting Frank has the right to know, but Wiley still refuses. MacGyver seemingly backs down but the puts his own plan into operation. He rents a tow truck and then cuts the coolant tubes on the Federal Marshals' primary car. He then buys a box of soda and pop rocks at a concession stand in the courthouse and uses them to create smoke in the ventilator shaft. When Wiley evacuates the building, he sends two of his men to take Frank to a safehouse. Their car breaks down, and MacGyver drives by. They requisition his tow truck and he keeps them occupied while Frank slips into the cab. MacGyver drives off with the car, leaving the Marshals behind. They stop another vehicle and follow, but MacGyver drives into an alley and dumps the car, blocking the pursuit.
Frank and MacGyver go to the hospital and discover that Joey has moved Katarina to the family estate. Frank insists on going there to follow his mother's dying wish. MacGyver advises against it, and Wiley arrives. He has a search warrant, but Vincent reveals they used their connections to get a judge to revoke it. Wiley sets up outside the manor, and Frank figures it's safe to go inside. Frank and MacGyver go over the fence and determine the security systems have been shut off. MacGyver waits while Frank turns himself over to his brother's thugs. As Frank sees his mother, Joey impersonates his brother's voice and calls Wiley, telling him he's changed his mind and is at MacGyver's. Using wiretapped conversations between Frank and Wiley, Joey convinces Wiley he is who he says. The Federal Marshals leave, and Joey turns the security systems back on and unleashes the attack dogs.
Katarina recovers consciousness and talks to Frank about his childhood and his promise to keep her safe. She says goodbye and then dies, and a tearful Frank goes to the window. He realizes that Wiley has left and signals to MacGyver. MacGyver runs for the house and grabs a pole and some string out of the garbage. He manages to jimmy an outside door open and get inside just ahead of the attack dogs. Inside, Frank tells Joey that their mother is dead. Joey takes his brother downstairs to finish him off. MacGyver rigs the pole and the string as a trip on the stairs. When Joey and his man Max go down the stairs, MacGyver and Frank run up the stairs and are forced to take refuge in the attic. They barricade the door but Joey is confident that they can't escape.
Wiley gets to MacGyver's apartment and realizes that he was tricked. He and his men head back to the manor.
MacGyver quickly builds a crude cannon out of a telescope, camphor balls, and cleaning fluid. He uses the cannon to fire a metal spike with wires attached, across the yard and into a tree on the other side of the fence. Using discarded pulleys, first Frank and then MacGyver ride the wire over the fence to safety. Joey and his men finally get through the barricade, and Joey can only note their father would be proud of Frank. Outside, Wiley and his men arrive, and MacGyver wonders if Joey has any regrets. He admits he does, but he didn't have any choice.