The Phoenix Foundation is supervising the disassembly of a Triton II ICBM missile as part of a cooperative program with the Pentagon to make nuclear missiles harmless. Pete supervises the operation from the control booth while MacGyver is working with the team on the first missile. He and Reese proceed while Pete explains the procedure to the disassembly committee. MacGyver removes the detonation primer charge and disconnects it, and the transfer team pulls up in a vehicle to transfer it to an underground bunker for detonation. The radiation levels are safe and the team removes its protective gear while MacGyver paints over the "Loaded" sign on the first missile.
After the committee leaves, Pete meets with the Ed Farrell, the Foundation chairman, and assures him everything is going well. He has a new project ready but Farrell tells him to take it easy before he suffers from burnout. The board meets and Farrell reports that they have persuaded President Amunde of Sambaga to make a first-time visit to America. Board member and intelligence director Matt Webber wonders why Amunde is coming there and Pete suggests Amunde wants to reconcile their difference, Webber isn't convinced, noting Amunde has been creating a terrorist organization. Farrell points out those are suspicions without confirmed evidence and Webber agrees to make sure Amunde has a good time. Another board member, Kennan, reports that Amunde will secretly staying at his private train car at Union Station. After the meeting, Webber notes that Amunde is a paranoid and Pete wonders why he's so deadset on believing Amunde is a terrorist. Webber notes that he lost several agents to one of Amunde's purported terrorist operations. However, he assures Pete he'll do whatever it takes to protect Amunde.
MacGyver is playing hockey and Pete is playing goalie and successfully blocking his shots. MacGyver is less than thrilled but insists Pete stay out there to skate off some stress. Pete is less than thrilled to hear everyone is trying to baby him but MacGyver insists that he find something to relax with. They have the defueling process to deal with the next day that is even more critical. Pete dares MacGyver to take a few more shots. MacGyver goes for it and sinks the next shot.
Webber arrives at his office and finds Nikki waiting for him. The two are romantically involved and Webber invites her to dinner. She turns him down, worried they might be getting too close too fast, and gives him her report on Amunde's security arrangements. Later, Webber meets with Ingers of the DSX and tells him they have an opportunity now that Amunde is coming to town. Webber disagrees with Pete and the board and Ingers is equally opposed to his superiors' stand on Amunde. They go to the train station and meet with Reese and Kelham of the NSA in a train car. They go over Nikki's report of the security arrangements and then resolve to capture Amunde, chemically interrogate him for all of his terrorist contacts, and then release him to be discredited. Reese asks about Pete and Webber assures him that there will be some changes at the Phoenix Foundation.
The next day, Pete and MacGyver supervise the defueling of the Triton missile. They remove the fuel and shut down the pump prior to engagement. The meters oscillate and a charge builds up. A fire starts and an evacuation order is called. The pump blows up and MacGyver rushes to help one man on fire. Pete looks at the devastation while the EMTs confirm the man MacGyver saved is okay. MacGyver checks on Pete, who is devastated by the chaos and doesn't know what happened.
Later, Webber and Reese report that there is no sign of sabotage and the accident was caused by a power surge at the point of disengagement that ignited the gas. Pete confirms he did a check but insists there should have been a second check, and accepts the blame for the accident. Farrell dismisses Webber and Reese and then admits he's surprised it happened under Pete. Pete wonders what he missed and Farrell warns that the government wants someone's head. Pete knows who it has to be and understands. Farrell suggests he take a short leave of absence but Pete points out it's too important for him to do that. He hands in his resignation and suggests Webber is ready to take over.
Later, MacGyver goes to Pete's home to talk to him after he disappears for a four-day weekend. Pete confirms that he resigned but MacGyver thinks he's overreacting. Pete disagrees, saying that three men died and eight more are in the hospital. MacGyver wants him back but Pete says that there's no going back. He thinks Webber will do fine but MacGyver thinks he's too gung ho. Pete admits he's had to face his limitations and tells MacGyver talk to Webber. MacGyver leaves, and Pete sits there alone.
Webber is busy moving into Pete's office and telling Nikki that he's going to give her a break by pulling her off the Amunde assignment. he wants her to take over as head of research. MacGyver arrives and Nikki leaves, and Webber offers MacGyver some environmental projects. MacGyver would rather review the defueling accident. Webber insists it's old news and there's nothing they can do for Pete. MacGyver insists on going ahead with his personal investigation.
Amunde arrives at Union Station in his train car. Webber welcomes him but Amunde isn't convinced he's sincere.
MacGyver returns to the defueling warehouse and talks to the security guard, Sam. Sam warns that the area is off-limits but lets MacGyver in to help out their mutual friend Pete. Nikki comes in and spots MacGyver, and realizes something is up. She points out that it's her job to check things out, and takes offense that MacGyver thinks she doesn't care about Pete. MacGyver apologizes and then spots something patched in as an interceptor that didn't fry when the rest of the pump burned up. He determines it's an electrical booster and concludes someone sabotaged the fuel pump to ignite when it was shut down, and set it up to look like Pete failed.
MacGyver and Nikki go to Pete's apartment to tell him the news but discover that he's gone. Nikki warns that MacGyver is working freelance but MacGyver warns that he's trying to protect her and suspects that Webber is involved in the sabotage. Nikki doesn't believe it and goes off on her own while telling MacGyver to do the same.
Webber and his team are preparing to take Amunde when Reese arrives to tell Webber that Nikki is at the train station coffee shop. Webber goes to see her and Nikki shows him the evidence. Webber promises to get to the bottom of it and then draws a gun and takes Nikki captive.
MacGyver gets a message from Sam and goes to the defueling station where Pete is looking over the debris. Pete says he's doing penance but MacGyver explains that someone sabotaged the pump. He tells Pete to take back his position but Pete insists that they should follow protocol and it's Webber's job to investigate. MacGyver explains that Webber has fired all of his division chiefs and scrapped Pete's entire agenda. When Pete hesitates, MacGyver wonders if Pete has really retired.
Webber's team take out Amunde's guards with tranquilizer darts and capture the president. Webber arrives with Nikki and tells her she should have taken the job in research he offered her.
Pete hacks into the Foundation files using the passkey MacGyver was supposed to turn in. The data confirms what MacGyver has claimed and shows that Webber has drawn up assault plans on Amunde's car.
Webber prepares to torture Amunde with a painful chemical injection to get him to reveal his terrorist connections. Nikki warns him he can't do it but Webber is unconcerned. He gives Amunde ten minutes to think it over while he deals with Nikki. Webber takes her outside where Pete and MacGyver ambush him and his men. Webber grabs Nikki and uses her as a hostage, but she disarms him. Pete goes after Webber when he flees while Nikki takes MacGyver to the mail car where the others are keeping Amunde. MacGyver prepares to pump steam from the train in through the vent.
Pete tackles Webber, who punches him repeatedly and boasts that he's much tougher. Pete gets the upper hand and takes him down.
MacGyver pumps the steam into the mail car. When the others come out, MacGyver takes them out and goes to see how Pete is doing. He discovers that Pete has loaded Webber on a baggage car and is wheeling him back. MacGyver assures him that he's still in his prime.
Later, Amunde makes a press statement noting that he might have done the same thing. MacGyver, Nikki, and Pete, watching the newscast, are less than amused. Nikki apologizes to Pete for falling for Webber's line and removes her ex-lover's personal items from Pete's office. Pete vows that he's going to take some time off to learn karate so no one ever takes advantage of him again.