MacGyver is dozing at his loft when a shadowy figure slips in through the door and moves to the couch while wielding an axe. The figure raises the axe and prepares to bring it down and MacGyver looks up at his archenemy, Murdoc. Murdoc brings the axe down and MacGyver wakes up from his nightmare to discover that no one is there. The phone rings and MacGyver answers: it's Murdoc, chuckling and wishing him pleasant dreams.
The Phoenix Foundation's new field manager, Cindy Finnegan, reports to Pete that MacGyver is showing signs of job-related stress accompanied by hallucinations. MacGyver arrives and Pete warns that Finnegan doesn't know MacGyver or Murdoc very well. Finnegan points out that Murdoc was found dead at the bottom of the mine shaft but MacGyver notes there wasn't enough left to make a positive identification. He insists that he's okay and Finnegan warns that ex-dictator Pablo Delasora of El Santori is arriving at the courthouse for the trial and MacGyver's position as head of security for Delasora is compromised. MacGyver insists that the security is already in place. Finnegan insists on double-checking MacGyver's precautions and Pete objects. However, MacGyver insists that Finnegan check and they leave for the courthouse. He tells her that her car hasn't been cleared through security and he'll drive.
MacGyver and Finnegan arrive at the courthouse and review the security procedures. However, they discover that the public has already gathered to see Delasora arrive. MacGyver speaks with Bob Stryke, the Federal chief, who reveals that Delasora's lawyer revealed announced his arrival to the media. Stryke introduces his assistant, Marietta Robles. Delasora arrives and Marietta complains about how he's gained weight while awaiting trial for helping his government loot the people's funds. The prisoner speaks out, claiming he was illegally kidnapped. MacGyver scans the crowd and sees Murdoc in the crowd, preparing to fire a dart gun disguised as a camera. MacGyver yells and the guards get Delasora down as the dart goes into the wall. MacGyver tackles the assassin only to discover that he's someone else. He tells Finnegan and the others that Murdoc was there but no one else saw the assassin. Finnegan calls Pete while Stryke tells MacGyver that there's no dart anywhere. Pete talks to MacGyver over the phone and tells him that the Foundation can't have any further controversy over the security arrangements. MacGyver insists that Murdoc isn't dead and Pete takes him off the assignment. He warns that he suspects Finnegan's job is to watch Pete's performance and she's already filed a report on MacGyver's obsession.
Back at home, MacGyver listens to a radio broadcast about the assassination attempt and the controversy surrounding the Phoenix Foundation involvement's with the security arrangements.
In a darkened room, Murdoc assembles a bomb.
That night, MacGyver's phone rings. He turns on the phone-tracing unit and answers it. Murdoc says he plans to make sure that MacGyver regrets ever killing him. Once Murdoc hangs up, MacGyver traces the call to 851 Dermot Road and drives there the next morning. There's an abandoned building at the address and MacGyver goes inside. He finds blocks of plastic explosive and newspaper clippings about the Delasora trial and the Foundation's involvement. There are also photos of Delasora, Stryke, and MacGyver. Finally he finds a photo of Marietta with a dart in it. MacGyver drives to the parking garage and stops her just as she gets in. He looks underneath and finds Murdoc's bomb attached to the underside. MacGyver cuts it loose but hears something rattling inside. He opens it and discovers that it contains a black pawn, and realizes the attempt is a distraction.
Murdoc, disguised as a waiter, delivers a cart of food to Delasora's hotel room. He leaves, going past Finnegan, while MacGyver calls Stryke and tells him to get Delasora out of the hotel. Stryke informs Finnegan about MacGyver's report and overrides her when she objects. She starts down the hallway just as the bomb goes off, wounding Delasora and kiling his guards.
Pete reports to the military that Delasora was in a different room and survived the bomb blast, although one Phoenix guard was killed. Marietta insists that Delasora was always good at surviving and thinks a trial is a waste of time. MacGyver wonders how Murdoc managed to miss his target twice. Finnegan informs everyone that her men found nothing at the address and still insists that Murdoc is dead and someone else is responsible. Stryke tells Pete that the Foundation is off the case because of concerns about Pete's capabilities. The government is flying in a crack Special Forces squad to reactive an old military base. They'll keep Delasora during the trial. After Stryke and Marietta leaves, Finnegan demands that Pete release MacGyver. Pete is forced to agree and fires MacGyver.
At his loft, MacGyver listens to the radio as Delasora accuses terrorists from the government who overthrew him of planting the bomb. Pete arrives and MacGyver admits he's been expecting him and that everything was a set up to get Finnegan off their backs. Pete explains that he still has to prove himself and despite the fact he's convinced that Murdoc is involved, Finnegan and the board have his hands tied. Now MacGyver can work on his own. They wonder who is employing Murdoc and suspect some of the high-security risks the government was worried about. Pete suggests that MacGyver go to the military base to check things out.
The next day, MacGyver sneaks up to the base and observes as Delasora casually strides around the facilities as officers salute him. Murdoc is present, dressed as a general, and MacGyver watches as Marietta is driven into the base as a prisoner and taken to the command center. MacGyver knocks out a guard and takes his base, and then slips in as an announcement goes out a test firing. MacGyver spots Delasora's soldiers preparing a missile for a test ignition. He approaches the missile and Stryke emerges to call him over to help. MacGyver tries to duck him and Stryke realizes something is wrong. He draws his gun and forces MacGyver to turn around.
In the command center, Delasora boasts to Marietta that he recognized her as a bureaucrat in his government who turned against him. Murdoc explains that Delasora plans to take back the capital of El Santori using the missile. Stryke brings MacGyver in and Delasora explains that Murdoc will be a general in his new government. Murdoc admits that HIT decided he was over the hill so he decided to join forces with Delasora. The missile is ready for launch and Delasora orders Murdoc to prepare a firing squad. MacGyver taunts him, noting that he's failed to kill MacGyver on his own and now he needs a firing squad. Murdoc agrees to shoot Marietta but asks permission to prepare a more imaginative way to dispose of MacGyver.
Murdoc takes MacGyver to the missile and explains that the body the authorities found was a fisherman that he killed and put in his place. The assassin boasts that his entire plan has been to use MacGyver to discredit the Foundation. Murdoc ties MacGyver under the rocket and explains that they'll fire it at the capital of El Santori so Delasora's men can move in. Everyone leaves and MacGyver tries to kick the booster out of alignment. When that fails, he kicks off his boot and throw sit at a nearby cart holding liquid nitrogen. The cart catches on an abutment and stops just short. He manages to grab his other boot and grabs the shoe string, and then uses it as a crude grappling hook to latch onto the cart's handle and pull it over the abutment. A tank of liquid nitrogen falls over and MacGyver opens the valve, freezing the rope so he can shatter it. He then throws rags into the missile's air intake valves and gets clear just in time.
Delasora orders Murdoc to finish Marietta off. As the assassin prepares the firing squad, the missile goes out of control and blows up. Murdoc realizes that MacGyver is responsible but Delasora orders Murdoc to take care of Marietta first. MacGyver drives up in a truck and rescues Marietta. As they drive away, Marietta says they need to go back to the command center to warn her people. Meanwhile, Stryke demands his money and Murdoc informs him his payment is in his car. Stryke gets in and opens the briefcase and finds an automated dart gun. It fires, killing him.
MacGyver drives to the command center to use the radio but Murdoc has anticipated him and arrives there with Delasora. Delasora has his soldier disarm Murdoc and admits that he always anticipated Murdoc would become a liability. As Murdoc is taken out, Delasora draws a gun and assures MacGyver and Marietta that his plan can still succeed without the missile. Gunshots ring out from outside the bunker. MacGyver uses a bottle of spray cleaner to short out a light bulb, distracting Delasora so he can knock the dictator out. He runs outside to check on Murdoc and discovers that the assassin killed the soldier who took him outside. Murdoc tries to escape on a jeep and MacGyver leaps on board. Murdoc brakes to a halt, throwing him off, but MacGyver manages to leap onto the hood. The assassin drives for a cliff and brakes, throwing MacGyver off again. Murdoc accelerates to run him over and MacGyver dives out of the way. The jeep goes over the cliff as Murdoc screams MacGyver's name.
Later, MacGyver is at his loft and wakes up, startled, as Pete comes in. Pete tells him that Delasora's troops have surrendered and the trial will start all over again. Finnegan sends her apologies and Pete figures she's coming along. When MacGyver points out his friend could have told him everything over the phone, Pete admits there's one more thing. He tells MacGyver that they didn't find Murdoc's body. The phone rings and MacGyver answers it. Murdoc chuckles and hangs up.