MacGyver receives a call from an old friend: Anthony Braddock a chemical and explosives expert formerly with British Intelligence. MacGyver once used his explosives to break out of prison, so Braddock is calling the favor. MacGyver meets Braddock at a warehouse on the docks, unaware that three terrorists are on Braddock's trail. Their leader, Lancer, sends Jules in to find Braddock while Tara drives the RV.
Braddock explains to MacGyver that he was forced to go on the run after Lancer hired him to prepare a revolutionary new explosive: a stable plastique that can be woven like cloth. Once he realized Lancer planned to use it to take out the members of Omega Force, an elite squad of U.S. anti-terrorists, he went on the run. Braddock knows that the assassination is planned for 4 p.m. the next day at the funeral of one of Omega Force's members, but he doesn't know how Lancer plans to hide the bomb.
Jules spots them and goes back and gets Lancer. The two men return and open fire, killing Braddock. MacGyver runs into the warehouse and Lancer figures he doesn't have a gun so they can go after him. MacGyver slaps two wooden slats down on the board to convince them otherwise and then makes a chemical smoke screen out of hull cleaner and ammonia. Lancer gets off a shot, grazing MacGyver's forehead and knocking him back out a window into the waters below. A stunned MacGyver manages to swim over to a passing trawler, the Damian, and climb on board. Lancer and Jules get the trawler's name as it moves out of firing range. Meanwhile, the trawler's captain, Carol Varnay, is trying to make a call to shore and discovers her radio is on the blink. She's unaware that she's picked up a passenger.
A few hours later, MacGyver has filed to turn up at the Phoenix foundation and Pete's secretary Helen checks the local police stations and hospitals for any word of MacGyver.
MacGyver manages to make his way to the bridge and collapses. Carol tends to his head injury and tries to find out who he is. MacGyver admits he doesn't know who he is or how he got shot. She tries to call the Coast Guard but her radio is still on the blink.
Lancer has Tara, the driver and computer expert of team, try to track down Carol's ship but the registration bureau is closed for the night.
The next morning, Carol arrives at Bristol Harbor 50 miles down the coast. MacGyver still has no memory of anything except that someone shot him, and insists that he can't go to the police. He checks his pockets but doesn't find any identification. However, he does get flashes of memory. Carol thinks he needs to see a doctor but MacGyver insists he just needs time to think.
Lancer returns to the warehouse. Impersonating a reporter, he talks to the policeman investigating Braddock's death. Lancer spots Pete and recognizes him as a former DXS operative. He takes photos of Pete and then approaches him and asks if one of his operatives was involved. A worried Pete denies any connection and talks to the police, while Lancer returns to the RV. Tara gets Carol's address and Lancer sends Jules to investigate.
As MacGyver's memories start to return, Carol's nephew Jason rides up on his bicycle. The chain has slipped the spokes and MacGyver quickly creates a guide out of the nametag.
As they drive to Bristol Harbor, Lancer explains to Tara that they need to determine if MacGyver passed on what he knows, and shows her the explosive: woven into a coat.
MacGyver and Carol eat and she talks about her family. She lost her brother and father in a storm and has stayed in the family business, even though she always wanted to go into marine science. MacGyver sees a Phoenix, AZ bumper stick and starts to get his memories back concerning the Phoenix Foundation. He remembers that it's in Los Angeles and that he knows the private number.
At Phoenix, Helen has obtained information about Braddock, including the fact he was connected to Lancer. They get a call from MacGyver but before he can say anything, Jules arrives and holds them at gunpoint. He forces them to leave but MacGyver knocks a rowboat on him and runs away with Carol. Jules reports back in with Lancer, and when it looks like his leader and Tara plan to turn against him, he warns he has enough to put them both away. Lancer apologizes and figures that MacGyver's amnesia won't last forever. They need to move quickly before Pete traces the calls and investigates.
After running a trace, Pete leaves for Bristol Harbor. He and Helen are absent when MacGyver tries to call again from Carol's house. MacGyver begins to wonder if he's some kind of criminal because of all the violence in his memories. Carol doesn't believe it and assures him he's a good guy.
Peter arrives at the phone booth and doesn't find anything. However, he spots Jason nearby and recognizes MacGyver's handiwork with the chain guide. He convinces Jason to tell him where he can find MacGyver.
Tara obtains Carol's address from the maritime records and Jules volunteers to dispose of MacGyver once and for all. Lancer obliges and once Jules is gone, Tara wonders what Lancer is up to. She suggests they leave now but Lancer refuses to blemish his reputation by reneging on a contract. He assures her that he has plans for MacGyver.
MacGyver regains more of his memories, including Braddock's warning that the explosive can be woven like cloth and that it'll be used at a cemetery. He remembers the name of the cemetery and calls Phoenix, but Jules arrives to kill them. There's a brief struggle and Carol runs, but Jules gets the upper hand. However, Lancer arrives and shoots Jules from behind. He then explains that he's Major Dawkins with Military Intelligence, and MacGyver's boss. Lancer explains that MacGyver's mission was to learn when the assassination attempt would take place. He already knows who the killer is: professional terrorist Peter Thornton.
Lancer and Tara take MacGyver in the RV to the cemetery. As they go, Lancer makes a fake radio call to assure the authorities they're on the way. He then explains that the Phoenix Foundation is a terrorist front and Pete has been trying to kill MacGyver for five years.
Pete arrives at Carol's house and she tells him what happened. She relates the cemetery name and Pete leaves to intercept MacGyver.
At the cemetery, Lancer takes MacGyver to the funeral site where Omega Force is gathered for their fallen comrade. He gives MacGyver a gun and orders to kill Pete when he sees him. Lancer sets the explosive coat down, sets the timer, and claims he's going to check perimeter security. Pete arrives and MacGyver intercepts him and prepares to shoot. Pete tries to get through to him, saying that he knows that MacGyver is uncomfortable with the gun. He reminds MacGyver of how he saved him from an avalanche and MacGyver finally gets his memories back. He gives Pete the gun and they go after Lancer. MacGyver spots the coat and realizes it's the explosive. He stuffs it into a metal planter and tosses it under Lancer's RV as he tries to escape. The vehicle is disabled and MacGyver fastens the door shut from the outside as the police arrive.
Later, MacGyver visits Carol and tells her about how the Phoenix Foundation performs special favors for him as payment. This time they've provided Jason with a new bike. Carol admits that MacGyver's amnesia has inspired her to let go of her own memories, and she plans to take night courses to get her degree in marine science.