Pete Thornton, an agent with the DXS, arrives on the docks to meet MacGyver as he returns on a ship from Eastern Europe where he's stolen a list of terrorists. An East German agent, Curt Neilson, is watching for MacGyver and spots Thornton as well.
MacGyver gets off the ship and stops to help a young girl, Lisa Allen, catch fish. He makes a lure for her and goes on his way. Thornton meets MacGyver and asks about the list, while Neilson and his assistant Barrett meet with their local thug, Crisp. They go after Thornton and MacGyver, and Thornton draws their fire so MacGyver can escape. Barrett shoots Thornton in the shoulder while MacGyver hides the list in a lamppost and knocks out Crisp. MacGyver runs into a cop but the man knocks him out: he's Polk, Barrett's accomplice in disguise.
Thornton gets back to DXS headquarters and confirms that Neilson is involved. He orders his agents to find the East German and MacGyver.
Neilson and his men take MacGyver to a warehouse. When they don't find the list on him and MacGyver refuses to reveal where he hid it, Neilson prepares to inject him with a poison. He explains that the drug will first induce dizziness, memory loss, and hallucinations for three hours, followed by pain. Finally, the drug will kill MacGyver after six hours unless Neilson gives him the antidote, a pill that he has in a metal cylinder. He injects MacGyver with the poison then puts on a wristwatch with a six-hour timer.
Neilson calls to tell his superiors he'll have the list while Crisp and Polk lock MacGyver up. Once he's alone, MacGyver rigs a makeshift catapult out of the bed, fastening the springs to the door. As the poison starts to kick in, MacGyver uses his belt to form a makeshift tube to redirect the water from the sink to the fuse box below. When it shorts out, Crisp and Polk figure MacGyver is responsible. When they go to the door, MacGyver releases the bedframe, which slams through the door and knocks the men back. MacGyver runs outside but collapses from the poison's effects. Neilson assures his men they have three hours before MacGyver recovers his memories and can call the DXS, but they need to find him.
As MacGyver revives and staggers down the street, Lisa and her friends spot him. They figure he's drunk but Lisa goes to help him in return for his help earlier. She offers to get a policeman but the delirious MacGyver remembers the fake policeman who ambushed him earlier and warns her not to involve the law. She takes him to the abandoned building where she lives, and has equipped with books and lights powered by a car battery. As she cooks fish for him, he gets her to talk about her past and how she left home to avoid an abusive father. Now she's studying so that she can get her diploma.
Neilson's men find Lisa's friends and learn that she found MacGyver and where she lives. At Lisa's home, MacGyver suffers hallucinations of Neilson coming in and smothering him with a pillow. When he wakes up, MacGyver begins to remember what happened. Looking at the watch, he realizes that he has an hour and thirty minutes left and remembers who he is and where he hid the list.
Neilson's men break in downstairs, setting off Lisa's makeshift burglar alarm. MacGyver hooks up an old TV tube to the car battery and places it on a chair in front of the door, then rigs jumper cables to complete the circuit when the door is opened. He and Lisa head for the roof and Crisp opens the door, causing a small explosion. Barrett and Polk come to investigate and they head up to the roof where they discover that MacGyver and Lisa have climbed down a fire hose and escaped. Once they leave, MacGyver and Lisa emerge from hiding and head for the docks to get the antidote. En route MacGyver tells Lisa to call Thornton and tell him what happened and where the list is hidden.
MacGyver sneaks up to the warehouse and knocks out Crisp. Inside, he rigs up several large water bottles from the ceiling by a rope, then sets up a wooden panel beneath them, sits down, and holds the rope with his foot. He sets off the smoke alarm and when Barrett and Polk, arrive, he offers to surrender. When he stands up, he releases the rope and the bottles bounce off the ramp and knock the men out.
Lisa calls Thornton and comes to the warehouse, while MacGyver chases after Neilson. The agent knocks him down and throws the metal antidote cylinder down a sewer grate. The weakened MacGyver manages to knock him out. He then grabs a metal rod and pounds it against a fire hydrant, temporary realigning the molecules and giving it a magnetic field. Reaching through the grate, MacGyver manages to snag the metal cylinder with the magnetized rod, pull it up, and take the antidote with two minutes to spare.
Later, MacGyver recovers the list and stops to visit Lisa. He explains that as payment for his mission, he's made an arrangement with Thornton to get her a government scholarship.