On behalf of the Phoenix Foundation, Pete is supervising the disassembly of Triton II ICBM missile for the Pentagon. MacGyver is working with a Foundation team lead by Reese to remove the detonation primer charge from the first missile. The team slowly proceeds and removes the primer charge and sends it to a bunker for safe detonation. Afterward, Pete meets with Ed Farrell, the Foundation's chairman. Pete's ready to take on a new project and Farrell warns him against burnout.
The Foundation board meets to discuss the situation with President Amunde of Sambaga, who is paying his first visit to America. The Foundation is in charge of security arrangement. The Foundation's intelligence director, Matt Webber, questions Amunde's commitment to peace, noting he's sponsoring dozens of terrorist organizations. Pete notes the evidence is circumstantial and is willing to give the Middle East ruler a chance. Farrell backs Pete and Webber agrees that he'll do a job no matter what his personal misgiving. They review the security plans and confirm that Amunde will be arriving at Union Station in his private car while the press is led to believe he's staying at a hotel. Afterward, Pete wonders why Webber is so against Amunde. Webber explains that some of Amunde's alleged terrorists killed several of his men, but promises he'll do his job and protect Amunde.
Later, MacGyver gets Pete to relax by having him play goalie against him in the hockey rink. Pete does surprisingly well, but isn't happy that MacGyver is trying to baby him. MacGyver also warns Pete against burnout and notes that the next step in the disassembly, the missile's defueling. Pete insists that he's fine and dares MacGyver to do his best. MacGyver sinks the next shot.
Webber goes to his office and meets with Nikki. The two are dating and Webber invites her to dinner. She tells him she's busy with Amunde's security arrangements and gives him her report.
Later, Webber meets with Ingers, a DSX operative. Both men are opposed to letting Amunde come to the country peacefully. They go to Union Station and the mail car they're using as a base of operations. Webber and Ingers with Kelham of the NSA and Reese from the Foundation's disarmament team. Now that they have Nikki's security plan, they plan to capture Amunde, torture him for information on his terrorist organizations, and then release him. If he reveals what happened, it'll be dismissed as more of his anti-American propaganda. Webber assures the others that he has plans for Pete.
The next day, Pete and MacGyver supervise the team as they defuel the missile. However, as the team removes the fuel and shuts down the pump, a charge builds up and an electrical short starts a fire. The pump blows up and MacGyver runs to help one man set on fire. He manages to save the man's life but three other men die and Pete admits he has no idea what happened.
The board meets, and Webber and Reese report that there is no sign of sabotage. It appears that an accident led to a power surge that ignited the fuel. Pete says that he did a check but blames himself for not conducting a second check personally. Farrell dismisses the others and warns Pete that the government is going to want someone fired. Pete knows who it is and assures Farrell that he has no choice but to hand in his resignation. As he leaves, he says that Webber is ready to take over his position.
A few days later, MacGyver goes to see Pete at his home. Pete confirms that he resigned, but MacGyver believes he should get his job back. Pete insists that he was responsible and he has no choice, even though MacGyver wants him back. MacGyver warns that Webber is too gung ho and doesn't know his limitations. Pete says that he knows his now and tells MacGyver to talk to Webber.
Webber is busy moving his personal items into his new office: Pete's. He tells Nikki that he's pulling her from the Amunde assignment and putting her in as head of research. As MacGyver arrives, Nikki expresses her condolences about Pete and leaves. Webber says he has some environmental projects for MacGyver to spearhead, but MacGyver would rather look into the accident. Webber says that it's over and done with and that there's nothing they can do for Pete. He notes that Pete may have known it was time to move on. MacGyver insists that he's going to handle the investigation first.
Amunde's train arrives at Union Station and Webber is there to greet him.
MacGyver goes back to the disssembly station and convinces the security guard, Sam, to let him take a look around. Nikki comes in, spots MacGyver, and takes offense at him involving himself in her department. However, MacGyver finds an electrical booster that wasn't burned up in the accident, and realizes it's not part of the pump mechanism. He figures that someone sabotaged the fuel pump and hoped the fire would destroy all the evidence, all in the hope it would make it look like Pete was incompetent.
MacGyver and Nikki try to inform Pete of their discovery but learn that he's disappeared. Nikki thinks they should go to Webber but MacGyver admits that he thinks Webber is involved since he has the most to gain. Nikki doesn't believe it and tells MacGyver to do what he has to while she does what she has to.
As Webber and his men prepare to capture Amunde, Nikki arrives to see Webber. He goes to see her in the empty station dining room and Nikki explains what MacGyver found. Webber takes her prisoner and takes her to the mail car.
Sam the security guard calls MacGyver and lets him know Pete has returned to the disassembly station. MacGyver goes there and tells him what he's learned. Pete insists they should follow protocol but MacGyver informs him that Webber has gutted Pete's old division. When Pete wonders what to do, MacGyver wonder if he really has retired.
Ingers, Reese, and Kelham use tranquilizer darts to knock out Amunde's guards. They capture Amunde as Webber arrives with Nikki.
Pete hacks into the Foundation computer and confirms what MacGyver said. They also find detailed assault plans for an assault on Amunde's train car.
Webber prepares to chemically interrogate Amunde and gives him ten minutes to consider. He then takes Nikki outside and prepares to dispose of her. MacGyver and Pete ambush him and Reese. Webber takes Nikki hostage but she elbows him in the gut. She breaks free and Webber runs off. Pete goes after him and Nikki and MacGyver to the mail car.
Pete manages to tackle Webber, who sneers and mercilessly beats Pete to the ground. The younger man moves in for the kill but the battered Pete fights back and knocks him out.
MacGyver pumps steam into the mail car, forcing Ingers and Kelham out. MacGyver takes them out and goes to see what happened to Pete. A weary Pete arrives, wheeling an unconscious Webber on a luggage cart. Pete wonders if he's getting too old for fighting but MacGyver assures his friend he's in his prime.
Later, MacGyver, Pete, and Nikki watch the news as Amunde makes a press statement. He half-jokingly says he might have done the same thing in Webber's position. Nikki apologizes to Pete for not believing him and takes out the last of Webber's personal items. Pete tells MacGyver he's taking some time off to learn karate so no one will beat him up again.