The three-person board of Homicide International Trust summons Murdoc before them. He meets them at a warehouse and is forced to go through a metal detector. After removing his numerous weapons, Murdoc stands before the board and points that they tried to kill him the last time they met. The board admits they worried he might compromise their operations after he decided to retire. Murdoc wishes to rejoin HIT, but the board members point out that he has never been able to kill MacGyver, a major threat to their operations. The assassin admits that he owes MacGyver a debt of honor because his nemesis saved his life and the life of his sister, Ashton. The board is unimpressed, and Murdoc admits they have a point. He agrees to kill MacGyver for them, but they warn that MacGyver might be too dangerous. Murdoc produces a non-metallic knife and throws it at them, pointing out that he cheats.
MacGyver comes home and discovers that Murdoc has laid out an expensive vegetarian meal for him. Murdoc is waiting and invites MacGyver to sit down, thanking him for saving his sister Ashton. As MacGyver takes a seat, Murdoc explains that Ashton died in a skiing accident in Switzerland, and he's now the last of his family. As MacGyver expresses his condolences, Murdoc explains that he's been reevaluating his life and is going back into business. The assassin activates steel manacles that trap MacGyver in his chair, and then turns a Cupid centerpiece toward MacGyver. Murdoc dips poison on the Cupid's arrow and runs a string from the arrow mechanism to a camera, while explaining that he is rejoining HIT and needs the money. Finally Murdoc puts a candle beneath the string and waits for it to burn through and trigger the bow and arrow. MacGyver asks what Murdoc wants and finally admits that he's beaten him. Murdoc releases the manacles and MacGyver rolls clear just in time. The assassin explains that he's now saved MacGyver's life, and they're even. Now he can kill MacGyver with a clear conscience. He quickly departs, firing a shot to deter pursuit.
The next morning, MacGyver calls to warn Pete that Murdoc is back. He tells his friend that he's going to go into hiding since Murdoc will strike at his friends, and Pete's blindness makes him a primary target. Pete reluctantly agrees and offers MacGyver a Foundation safe house in the mountains and a car from the company pool. MacGyver accepts, unaware that Murdoc has tapped the phone lines and is listening in.
As MacGyver drives to the safe house, he finds Murdoc parked on the road, armed with a bazooka. Before he can drive away, Murdoc opens fire, blasting open the car. The assassin moves in only to discover that MacGyver has managed to escape. However, he's left behind his money, Swiss Army knife, and Foundation ID. Murdoc takes everything and goes the injured MacGyver, who is stumbling through the woods past an abandoned mine shaft. MacGyver gets to a campground and a girl, Amy Walker, spots him. She goes to get her mother, Suzanne, and Suzanne comes back with a gun. She demands to know who MacGyver is but he admits he can't remember and then collapses. Murdoc looks on from the woods and watches as they take MacGyver to a guest cabin.
MacGyver wakes up from dreams of the assassination attempt to find Suzanne binding his wounds. She is clearly suspicious of him and his claim that he lost his memory and identification in an accident. Murdoc listens in from outside and realizes what's happened to his enemy.
Suzanne explains that the owner hired her to watch the campground during the dead season and no one else is there. Suzanne locks MacGyver in the cabin, while Amy insists that she doesn't think MacGyver works for her father. Suzanne explains to her that they can't take any chances. They go back to the lodge where Murdoc is stealing a bite to eat. He slips outside before they can spot him. Suzanne sends Amy out to tend to the canoes while she tries to call the doctor, only to discover the phone lines are dead.
Murdoc prepares to break in to the guest cabin and finish off MacGyver, but sees Amy slip in through a loading hatch in the wood box. He pauses and then tampers with MacGyver's ID, replacing the photo with one of his own.
Inside, Amy watches over MacGyver. He wakes up from another vague dream about Murdoc and Amy asks if her father sent him. MacGyver admits he doesn't remember but promises not to tell anyone that she and her mother are hiding there.
Suzanne checks the junction box and discovers that the phone lines are cut. She thinks MacGyver is responsible and runs to the guest cabin, but Murdoc grabs her and pulls her away. He tells her that his name is MacGyver and he works with the Phoenix Foundation. He's on the trail of a dangerous assassin named Murdoc who matches the real MacGyver's description. He warns that if Amy is in the guest cabin, she's in terrible danger, and asks Suzanne to let him handle the dangerous situation.
In the guest cabin, Amy explains that her father was awarded custody of her thanks to his cadre of high-priced lawyers. He sent men to capture her and Suzanne took her into hiding.
Outside, Murdoc has Suzanne give him the gun and asks her to get Amy out of the cabin without letting on she knows who "Murdoc" really is. Amy slips out the way she came before her mother arrives. When Suzanne enters, she realizes Amy was there and apologizes. MacGyver says that he understands that Amy is lonely and doesn't have anyone else to talk to. He promises not to tell anyone that the Walkers are there, but notes that their life on the run isn't doing Amy any good. Suzanne snaps at him and leaves.
Suzanne goes back to the lodge where Murdoc is beginning to lose his temper with a suspicious Amy who doesn't believe MacGyver is an assassin. Murdoc tells Suzanne to take Amy into town and give him the keys to the guest cabin. As Suzanne takes her daughter to the car, Amy runs off, insisting that the real Murdoc is going to do something to her new friend.
Murdoc goes into the cabin and claims he's the doctor. However, he sets up a camera and attaches it to his pistol, and MacGyver quickly realizes something is wrong. Murdoc explains that his killing shot will activate the camera, capturing MacGyver's death on film and proving once and for all that Murdoc was able to best him. Amy arrives and pounds on the door, and MacGyver hits the distracted assassin with a chair and leaps through the door. He tumbles down the hill and Amy runs after him. Murdoc comes out and finds Suzanne waiting for him with her shotgun. When he refuses to surrender, she tries to shoot him but discovers that he removed the shells earlier. Murdoc calls out to MacGyver, saying to meet him at the abandoned mine if he wants to save Suzanne's life. He leaves for the mineshaft, goes inside, and finds a deep elevator shaft.
Amy picks up the shotgun and prepares to go after her mother. MacGyver stops her, takes the shotgun, and tells her to show him where the ammunition is. He awkwardly loads it and tells Amy to ride into town on her bicycle to notify the police. He goes through the woods and finds his Swiss Army knife stuck into a tree. Removing it, MacGyver proceeds to the mine and goes down the main shift. He comes up against a web of wires, attached to an explosive device. Murdoc steps out and dares MacGyver to shoot him. MacGyver tries but, despite his amnesia, realizes that he can't.
Murdoc activates the mine elevator which rises out of the shaft. Suzanne is tied to the bottom. Murdoc explains that if MacGyver doesn't get past the wires, the elevator will drop. To add a time element, Murdoc lights a fuse that will set off the explosives destroying the elevator cable. MacGyver wonders how he's supposed to stop it and Murdoc explains that he hopes the pressure will bring back MacGyver's memories so he doesn't have to kill a muddle-headed amnesiac.
Murdoc leaves the chamber and MacGyver comes up with an idea. He opens the shotgun into an L shape, props it on the cart tracks, and removes the shotgun shell. He then cuts open the shell and hammers the shot into flat discs. Finally he ignites the gunpowder, heats the discs, and uses them to weld one wire running across the tracks to either side of the shotgun. Once the shotgun is supporting the wire, MacGyver cuts the piece in the center of the L and slides through the resulting passage.
MacGyver runs to the fuse and pulls it out, only to set off a second fuse higher up that burns toward the mine elevator. It also ignites off writing on a board, revealing the words "R.I.P. MacGyver." MacGyver finally remembers who he is and what happened. Murdoc steps out and prepares to kill him with a hand crossbow. MacGyver blocks the shot with the board and jumps Murdoc. He manages to throw Murdoc into a side tunnel, burying him under rubble, and then runs up to the elevator car. As he cuts Suzanne free, Murdoc frees himself, draws a knife, and comes after his enemy again. Suzanne spots him and kicks him back onto a pile of rope as MacGyver finishes freeing her. The fuse reaches the explosive, cutting the cable. As the elevator car plummets into the depths, Murdoc steps forward to finish off MacGyver... and the rope attached to the car catches on his leg. He's pulled down into the shaft, screaming MacGyver's name.
Later, the local sheriff and his men are searching the mine while Suzanne tells MacGyver that she's going to try and work things out with her husband. The sheriff comes over and tells MacGyver that there's no sign of Murdoc. MacGyver isn't surprised.