MacGyver is dozing on the couch at his loft when a shadowy figure breaks in and comes over to his side. The figure raises an axe, and MacGyver wakes up just in time to see who it is: Murdoc. MacGyver wakes up and realizes the whole thing is a dream. However, the phone rings and when MacGyver answers, Murdoc is on the other end, wishing him pleasant dreams.
The next day, Pete is receiving a report on MacGyver delivered by Cindy Finnegan, the Foundation's new field manager. She informs Pete that the psychiatric report shows that MacGyver is suffering job-related stress since Murdoc's death. MacGyver arrives as Pete notes that she doesn't understand MacGyver very well. Finnegan notes that Murdoc's corpse was found, but MacGyver notes there wasn't enough left to make a positive identification and Murdoc has survived certain death before. She insists that MacGyver is compromised as head of the Foundation security team making sure that Pablo Delasora, the ex-president of El Santori, stands trial for his crimes. MacGyver notes that the security is already in place and Finnegan wants to double-check the arrangements.
At the courthouse, MacGyver and Finnegan review the security procedures. Everything is in place but they discover that Delasora's lawyer has notified the media. MacGyver meets with Bob Stryke, the Federal prosecutor, and his assistant, Marietta Robles. As Delasora arrives, Marietta complains about how he is prospering as always, safe in a comfortable cell with three meals a day. As Delasora proclaims his innocence to the media, MacGyver spots Murdoc, disguised as a reporter, preparing to shoot Delasora with a hidden dart. MacGyver yells out an alert and the assassin misses. MacGyver gives chase only to discover that Murdoc has disappeared as if he had never been there.
Afterward, MacGyver tries to find someone who can substantiate his story but no one else saw Murdoc and there's no trace of the dart. Finnegan assumes MacGyver is hallucinating and calls Pete, who has no choice but to take MacGyver off of the security detail. Pete warns his friend that the Board has assigned Finnegan to review his suitability to keep his position given his eye condition and she's already filed a report on MacGyver.
That night, Murdoc calls MacGyver again, promising that he'll regret killing him. MacGyver traces the call to an abandoned building. Inside he finds blocks of C-4 and newspaper clippings about the Foundation's controversial handling of security for the federal trial. Thee are also photos of Stryke, Delasora, and MacGyver. Finally, MacGyver finds a photo of Marietta with a dart in it. He dries to the parking garage where she's getting into her car and stops her just in time. He searches the bottom of the car and finds a metal bomb. He carefully removes it only to discover that the only thing inside is a chess piece, a black pawn. MacGyver realizes that Murdoc has set up the whole thing as a distraction.
At the hotel where Delasora is being kept for trial, a disguised Murdoc delivers a cart of food to the dictator's room. He leaves just as MacGyver calls Stryke and notifies him about the fact Murdoc is going after Delasora. Finnegan angrily goes to check on Delasora just as the bomb explodes. One Foundation agent, a friend of Pete's, is killed but Delasora was in a different room and survives the assassination attempt. Afterward, Marietta complains that Delasora has survived again while innocent people die. Finnengan reports that her people found nothing at the abandoned building and figures that MacGyver is still hallucinating. The government takes the Foundation off of case and Stryke informs Pete that they're calling in a Special Forces squad to reactivate an abandoned military base and keep Delasora there. Finnegan tells Pete to do his duty and he has no choice but to fire MacGyver.
MacGyver is at his loft when Pete arrives. Pete confirms that the firing was a setup just as they planned and now MacGyver has a free hand to investigate. However, he warns that despite the fact they're both sure Murdoc is involved, Pete's job is at risk and the board has tied his hands. He suggests that MacGyver check up on the military base.
The next morning, MacGyver approaches the base and watches as Delasora casually walks around while the guards salute him. Finally the dictator meets with Murdoc, wearing a general's uniform. MacGyver knocks out a guard, steals his uniform, and sneaks into the base to investigate a missile that the soldiers are testing for launch. Before he can do anything, Stryke comes out of the command center, spots MacGyver, and captures him.
Delasora's people have captured Marietta as well, who was a bureaucrat in Delasora's government and helped the breles against him. MacGyver is brought in and Murdoc explains that Delasora is going to launch the missile against the capital of El Santori and then march his men in. The assassin admits that HIT let him go because of failures so he's accepting the position of general in Delasora's new army in return for helping him retake his presidency. Delasora orders a firing squad to dispose of MacGyver and Marietta but Murdoc wants to give MacGyver a more imaginative death. He fastens him to the missile platform and departs with Delasora and his men to execute Marietta. Once he's alone, MacGyver kicks off one boot and hits the brake switch on a cart holding canisters of liquid nitrogen. It rolls toward MacGyver but jams on an abutment. Throwing his other shoe while holding onto the shoelace, MacGyver manages to hook the cart handle and pull it the rest of the way. He then uses the liquid nitrogen to freeze his ropes and break free. Finally he jams rags into the missile's air take valve and goes after Marietta.
As Murdoc oversees the firing squad and orders them to fire, MacGyver arrives in a truck and rescues Marietta. He drives away and Murdoc realizes where he's going. However, Stryke panics and demands his payment. Murdoc gives him a briefcase with a rigged dart gun that kills him.
MacGyver and Marietta start to send a signal to the capital but Murdoc and Delasora arrives. Murdoc prepares to kill his archnemesis but Delasora betrays him, anticipating that the assassin would become a liability. He has one of his soldiers take Murdoc outside to shoot him and assures Marietta and Macgyver that his plan can still succeed once he signals his soldiers to move on the capital. They hear a gunshot outside. MacGyver uses a bottle of spray cleaner to shatter an overhead light bulb, distracting the dictator and giving him the chance to knock Delasora unconscious. He runs outside and confirms that Murdoc killed his guard. The assassin drives away in a Jeep and MacGyver leaps on. Murdoc drives toward a cliff to try and throw him off and MacGyver is knocked to the ground. The assassin tries to run him over but MacGyver dives aside and Murdoc goes over the cliff.
Later, MacGyver is at his loft and wakes up, startled, as Pete comes in. Pete tells him that Delasora's soldiers have been captured and the dictator's trial will continue. Finnegan has apologized and Pete and MacGyver will keep their jobs. MacGyver wonders what Pete is leaving out and his friend explains that there was no sign of Murdoc's body. Pete insists that the tide could have washed the body out but MacGyver isn't so sure. Sure enough, Murdoc calls to give one ominous chuckle before hanging up.