A shadowy figure with a death's head ring arrives in a darkened warehouse: Murdoc. A woman tells him to remove his weapons and go through a metal detector. It reveals he has plenty of other weapons and Murdoc discards a variety of guns, handcuffs, brass knuckles, knives, and grenades. He walks back through the metal detector and three members of the board of Homicide International Trust reveal themselves. They call the meeting to order and welcome Murdoc back. He notes they tried to kill him the last time and they admit they were worried he would compromise HIT's operations. Now Murdoc wants to rejoin them. They note that they can't tolerate failure and he has failed to kill MacGyver repeatedly. Murdoc admits that Murdoc helped rescue his sister and saved his life, and he owes a debt of honor. When the board notes that there is no honor in their business, Murdoc concedes the point and agrees to kill MacGyver. When the board suggests that MacGyver might be too formidable, Murdoc notes that his opponent fights fair. He then produces a plastic knife and throws it at the board, just missing them.
MacGyver returns home to his houseboat to find an elegant dinner set up for him. Murdoc is at the head of the table and says he's there to thank MacGyver for saving his sister Ashton's life. MacGyver takes a seat and Murdoc explains that Ashton was killed in an avalanche while skiing in Switzerland. She was the last of his family and Murdoc explains that he's reevaluated his life and is going back to business. He hits a switch, causing manacles to trap MacGyver's arms. Murdoc then ties a string to the bow of a Cupid statue while explaining that he needs the money and is rejoining HIT. MacGyver notes he's breaking his word but Murdoc tips the arrow with cyanide and ties the string to a camera. Finally he puts a candle beneath the string holding the arrow so it'll burn through and release the arrow. MacGyver admits that Murdoc has beaten him and Murdoc releases him just in time. The assassin explains that now that he's saved MacGyver's life, they're even. Now it's just business, and he'll hunt MacGyver with a clear conscience. He leaves and fires a warning shot when MacGyver tries to go after him.
The next morning, MacGyver calls Pete to warn him that Murdoc is on the loose. MacGyver plans to go into hiding, much to Pete's surprise. He doesn't want anyone else getting hurt in the crossfire. Pete insists he can take care of himself but MacGyver notes he still needs his eye operation and can't take the chance. Pete reluctantly agrees but says his friend can use a Phoenix safehouse and a pool car. They're unaware that Murdoc is listening in, impersonating a telephone repairman.
MacGyver drives to Lookout Mountain but finds Murdoc waiting for him on a bazooka. MacGyver backs up but before he can get away, Murdoc fires, blowing up the car. However, when MacGyver moves in to investigate, he finds that MacGyver has escaped but left his money, Swiss Army knife, and ID behind. Murdoc takes everything and starts tracking MacGyver through the woods.
An injured MacGyver staggers through the woods past an abandoned mine shaft. He keeps going as Murdoc closes in and arrives finds a campground. A girl, Amy sees him and goes to get her mother Suzanne. Suzanne gets her shotgun and demands to know who he is. MacGyver says he can't remember and then collapses. Amy wonders if her father sent him and Suzanne admits she doesn't know. Murdoc arrives and watches as they take the unconscious MacGyver to a guest cabin.
MacGyver wakes up to find Suzanne tending his wounds. She notes that he doesn't have any ID but all MacGyver can remember is an accident and an explosion. Outside, Murdoc watches through the window and realizes what's happened. Meanwhile, Suzanne explains that the owner hired her to watch the campsite over the winter and it's the dead season. Suzanne leaves with her daughter and locks MacGyver in. Amy admits that she likes MacGyver and doesn't think he works for her father, but Suzanne warns that they can't take any chances. They go back to the mess hall where Murdoc is hiding. He slips out while Suzanne says that they have to be careful and won't always have to live in hiding. Amy goes out to cover the canoes and Suzanne tries to call the doctor but discovers the phone lines are dead.
Murdoc goes to the guest cabin and starts to shoot the lock off. However, he hears Amy and discovers her sneaking into the cabin. Murdoc gets an idea and replaces the photo on MacGyver's Foundation ID with his own. Meanwhile, Amy watches over MacGyver, who is having another dream of the crash. He wakes up and Amy asks if her dad sent him. She explains that she wants to stay with Suzanne and MacGyver promises not to tell anyone that they're hiding out there.
Suzanne discovers that someone cut the phone lines and runs to the cabin. Murdoc grabs her and explains that he's MacGyver and works with the Phoenix Foundation. He's on the trail of a professional killer named Murdoc, and describes MacGyver. He warns that Amy is in terrible danger if he's with "Murdoc." Suzanne gets her gun and Murdoc warns that "Murdoc" is full of tricks.
Amy explains that her father spent a lot of money on lawyers and won custody. He sent men to take her and she just barely escaped, and then Suzanne went into hiding with her. She doesn't believe that MacGyver is one of her father's men.
Murdoc tells Suzanne to leave him the gun and go get Amy of the cabin. She hands the shotgun over and unlocks the cabin. Amy slips out and Suzanne comes in. She claims she called the doctor and MacGyver admits he still doesn't remember anything. Suzanne realizes that Amy slipped out and apologizes, but MacGyver points out that the girl is lonely. He promises not to tell anyone and Suzanne starts to leave, but MacGyver suggests a life on the run isn't any good. Suzanne tells him it's none of his business, briefly giving MacGyver a flash of memory and Murdoc saying "strictly business."
Suzanne goes back to the mess hall and finds Amy with Murdoc. Murdoc repeats his story but Amy insists that MacGyver isn't a criminal. He tries to reassure her but Amy isn't buying it. Murdoc tells Suzanne to take Amy to town and leave him the keys. He assures her that he can handle "Murdoc." As Suzanne takes Amy to their car, the girl insists that she doesn't trust "MacGyver" and thinks he'll do something awful to "Murdoc." She runs back to the cabin and Suzanne goes back into the mess hall to get "MacGyver." Murdoc has already left and Suzanne grabs her shotgun.
Amy watches as Murdoc goes into MacGyver's cabin, MacGyver assumes he's the doctor and is surprised when Murdoc sets up a camera and takes out a gun. He explains that the shot will activate the camera and prove to HIT that he's not over the hill. Amy comes to the door and listens in as Murdoc boasts of his plans. Amy pounds on the door, distracting Murdoc, and MacGyver hits him with a chair and jumps through the door, rolling down the hill. Amy goes after him and they run into the woods. As Murdoc leaves, Suzanne arrives and tells Murdoc to drop his gun. She tries to shoot and discovers he removed the shells. Amy calls out for her mother and Murdoc calls out to say he'll be keeping Suzanne and MacGyver should meet them at the abandoned mine.
Amy grabs the gun and starts to go after Murdoc. MacGyver stops her and considers the gun, and then has Amy take him to the lodge where the shells are kept.
Murdoc takes Suzanne into the mine and discovers a deep vertical shaft. Suzanne realizes that he's the Murdoc that he described.
MacGyver hesitantly puts the shells into the shotgun as Amy asks to go with him. He tells her to go to the nearest phone and call the police, and then heads for the mine.
Murdoc rigs up an explosive device to the support beams. Meanwhile, MacGyver discovers his Swiss Army knife, stuck into a tree stump. MacGyver takes it and then continues to the mine. Inside the entrance he finds a web of wires. Murdoc is on the other side, and warns that any attempt to cut the lines or put pressure on them will set off the explosives. MacGyver aims the shotgun and Murdoc dares him to fire. When MacGyver hesitates, Murdoc tells him that it isn't in his blood. The assassin then brings up the shaft elevator with Suzanne tied to the bottom. He explains that if MacGyver doesn't get past the wires, the elevator will drop to the shaft. Murdoc lights a fuse and explains the elevator will also drop when the fuse sets off the explosives. MacGyver has no idea how to stop it and Murdoc admits that he wants to beat the real MacGyver, not an amnesiac.
Murdoc leaves and MacGyver tries to figure out a way past the wires. He notices that one wire passes over the mine tracks. MacGyver opens the shotgun and uses his Swiss Army knife to cut open one of the shells. He flattens the slugs with a rock and separates the powder. he then uses the L-angle of the broken-open shotgun to make an archway. Finally he heats the flattened slugs in the burning gunpowder and then applies the melted metal to weld the wires to both sides of the shotgun. Once they're welded, MacGyver cuts the wire in-between and crawls through the gap.
On the other side, MacGyver climbs up and pulls the fuse loose. That sets off a new fuse closer to the elevator and ignites a sign saying "R.I.P. MacGyver." MacGyver finally remembers his own name as well as Murdoc. Murdoc steps out, satisfied that he can now kill MacGyver in full. He shoots a crossbow bolt at MacGyver, but MacGyver blocks it with the R.I.P. sign. The two men struggle as the fuse burns closer to the elevator. MacGyver finally shoves Murdoc into a mine entrance, burying him in rubble, and then climbs up to the elevator. He cuts Suzanne free while Murdoc frees himself and comes after MacGyver with a knife. Suzanne kicks him back into a pile of rope and MacGyver gets her free. The elevator car plummets down the shaft and the rope wraps around Murdoc's leg, pulling him down.
Later, Suzanne admits that she and Amy are going home. She'll try to work things out but if not, he's in for a fight. The sheriff comes over and tells MacGyver that there's no sign of Murdoc. He figures no one could have survived that fall but MacGyver isn't convinced.