MacGyver meets at a warehouse the docks with Anthony Braddock, a chemist and former member of British Intelligence who once helped MacGyver out of a tight spot. Now Braddock needs help and wants MacGyver to come alone. Outside, three terrorists on Braddock's trail pull up in an RV. Their leader, Lancer, sends his man Jules in to find Braddock. Braddock informs MacGyver that he's been on the run because Lancer hired him to prepare an explosive. Meanwhile, Jules reports back to Lancer and his assistant, Tara, that Braddock is meeting with MacGyver. Lancer and Jules go in as Braddock explains that he created a stable explosive that can be weaved like cloth. He discovered that Lancer plans to use it to assassinate high-ranked officials in the U.S.'s anti-terrorist brigade, Omega Force. Braddock explains that the assassination will take place at a funeral tomorrow at 4 p.m., but has no idea how Lancer will disguise the explosive.
Jules and Lancer break in and open fire, killing Braddock. MacGyver makes a run for it and they figure he doesn't have a gun because he didn't use it. However, MacGyver slaps two boards on the ground to convince them otherwise and slow them down. He creates a chemical smoke screen but Lancer gets off a shot, grazing MacGyver in the head and knocking him through a window into the water below. A nearby fishing boat, the Damian
, passes nearby and a woozy MacGyver manages to pull himself onboard. Lancer and Jules make their way through the smoke screen and see the boat departing out of range. They get the trawler's name and leave to trace it. The ship's captain, Carol Varnay, tries to make a ship-to-shore call but is unable to get through, unaware that MacGyver has collapsed on the deck.
That night, a worried Pete has his secretary Helen check the hospitals and police but there's no word of MacGyver.
MacGyver stumbles onto the bridge of the trawler and Carol demands answers. He says he doesn't know who he is and then collapses. Carol tries to call the Coast Guard but her radio still doesn't work. She tends to MacGyver's head wound. On shore, Lancer has Tara try to access the computer files but they're shut down for the night.
The next morning, Carol pulls into dock at Bristol Harbor as MacGyver wakes up. He still has no idea who he is or how he got on the boat: all he can remember is that he was shot. Carol insists that she's going to drop him off with the police as soon as they get to shore. MacGyver goes through his pockets but doesn't find any identification. Once on shore, MacGyver sees a welder working and remembers when he burned open an armored car, then set off explosives at a nuclear plant. However, he refuses to go to a doctor, saying he just needs time to think.
Lancer impersonates a reporter and talks to the police lieutenant investigating Braddock's death. Pete arrives and Lancer takes photos of him, recognizing him as a former government operative. He approaches Peter and asks if MacGyver contacted him. Back in the RV, Tara comes up with Carol's name and Lancer sends Jules to investigate.
As Carol and MacGyver head out, MacGyver sees more things that stir his memories. Carol's nephew Jason comes by with his broken bike. MacGyver takes the nametag off the bike and uses it to make a makeshift chain guide. Meanwhile, the assassins drive toward Bristol Harbor and Lancer worries that MacGyver may have passed on his information. He informs Tara that he already has Braddock's explosive: woven into the lining of a coat.
As they eat, Carol talks about her family and how she lost her father and brother in a storm several years ago. She explains that she wants to get into marine science but the fishing life and memories of her family have a hold on her. MacGyver notices a Phoenix, AZ bumper stick and starts to remember the Phoenix Foundation. Carol tries to spur him into remembering and he realizes it's in Los Angeles. He tries to remember Pete's private number. Meanwhile, at Phoenix Helen informs Pete that his government contact Sam proved reluctant until she applied a little persuasion. Sam passed on that Braddock is tied to Lancer, an assassin. They're interrupted when MacGyver calls Pete's number. However, before MacGyver can say anything, Jules arrives and takes them away at gunpoint. As they walk down the pier, MacGyver knocks over a boat on the man and they run for it.
Jules returns to the RV and tells Lancer what happened. Lancer isn't thrilled but Jules warns that he has enough on them to put them away if they turn against him. He assures Lancer and Tara that MacGyver doesn't remember anything and didn't warn Pete. Lancer figures that MacGyver's amnesia won't last forever and Pete will trace the call, then come looking for his friend.
Pete completes the trace and drives to Bristol Harbor. Meanwhile, MacGyver and Carol go to her house and try to call Pete but he's no longer there to answer. MacGyver wonders if he's a criminal because of all his violent memories but Carol doesn't believe it. Meanwhile, Pete arrives at the phone booth and spots Jason nearby. Jason is wary of talking to strangers but Pete provides a description. Pete notices the makeshift chain guide and recognizes MacGyver's handicraft.
Tara finally gets Carol's address and Jules insists on going after them before they can identify him to the police. Once he leaves, Tara asks what he's up to and Lancer insists he's going to fulfill the contract, and use MacGyver to get Pete.
At Carol's house, MacGyver notices a photo of her father with a big fish and remembers fishing with his grandfather and finally the attack at the warehouse. He also remembers Braddock talking about the cloth-weave bomb at the cemetery. MacGyver realizes that Braddock is dead and remembers the cemetery name. He starts to call the Phoenix Foundation again but discovers the phone is dead. Jules arrives and prepares to shoot them. MacGyver attacks him so Carol can escape, but Jules knocks him down. However, Lancer arrives and shoots Jules dead, then identifies himself as MacGyver's boss Major Dawkins in Military Intelligence. MacGyver only remembers the cemetery and Lancer says that MacGyver's assignment was to determine when the hit was going down. Lancer informs him that they have a suspect: a professional terrorist named Peter Thornton.
Tara and Lancer take MacGyver to the cemetery in their RV and Lancer makes a fake radio call to the authorities. Once he's done, Lancer claims that the Phoenix Foundation is a front for a terrorist organization and Pete has been trying to kill him for five years. Meanwhile, Pete arrives at Carol's house and tells her about the assassination. She remembers what MacGyver said about the cemetery and Pete departs.
Lancer, Tara, and MacGyver arrive at the cemetery and Lancer grabs the rigged coat. He gives a gun to MacGyver and tells him to shoot Pete if he arrives. They go to the gravesite and Lancer secretly activates the trigger on the coat. He puts the coat down and leaves, claiming he's going to check perimeter security. Pete pulls up and spots MacGyver, who sees him coming. MacGyver has vague memories of Pete shooting someone. He intercepts Pete and draws the gun. Pete tries to take out a photo of the two of them together but MacGyver refuses to let him. Pete tries to get through to him, pointing out he hates guns and reminding him of the time he saved him from an avalanche. MacGyver remembers and gives Pete the gun, then tells him about Lancer. Pete clears the area while MacGyver remembers what Braddock said about weaving the explosive like cloth. He spots the coat and puts it in a planter, then throws the bomb underneath the RV as Tara and Lancer drive away. The bomb goes off, bringing the RV to a stop and stunning the two assassins long enough for MacGyver to secure the door.
Later, MacGyver visits Carol and tells her about how the Phoenix Foundation pays him off in favors. This time they provide a new bike for Jason. As the boy rides off, MacGyver thanks Carol for helping him and she thanks him for coming to term with her memories. She plans on taking night classes to get a degree in marine science and promises to invite MacGyver.