Amy Austin is the Director of Research at the Westport Nuclear Processing Plant. Amy is working when she gets a call from the state police telling her that the plant's general manager, Gerald Hillman, died in a car accident. Amy gets out a file on the disappearance of 235U radioactive material, a file she copied to Hillman. She tries to make a phone call, unaware that a figure in a protective suit has cut her phone line. She goes out into the plant and the figure follows her. Amy runs to the waste disposal chamber and hides the file behind a pipe, then goes to a plant phone. She gets an outside line and calls an old friend: MacGyver.
MacGyver is at home playing table hockey with a friendly neighbor, Susan. The answering machine picks up the call and Amy comes on asking for help. MacGyver immediately takes the call and Amy explains that someone is trying to kill her and already killed her boss. She apologizes for involving him but MacGyver assures her that's he'll be there. Amy tells him to meet them at "their beach," but is forced to run off when the figure comes after her.
The next day, MacGyver arrives at his and Amy's special spot at Westport Beach. He remembers back to when he and Amy were an item, but he wanted to travel the Mediterranean on a tramp freighter and she wanted to stay and build a future together. MacGyver insists on going and Amy drove away.
In the present, MacGyver sees a woman pull up in Amy's car. she waves to him… and then the car explodes. The police arrive and MacGyver examines the wreckage. Another old friend, Tim Wexler, comes by and says that Amy didn't show up at the plant where they both worked. MacGyver doesn't believe the explosion was an accident, and talks to the local police chief, Ed Train. Train notes that Hillman died the night before. MacGyver shows them the gas tank and a hole made by an explosive bullet. Tim admits that Amy wasn't really close to anyone and says the funeral will be the next day.
MacGyver attends the funeral. However, as he gets in the car he finds someone waiting for him in the back: Amy. She tells him to drive to her parents' house and explains that she sent her roommate to get MacGyver. As MacGyver tries to comfort her, Amy explains that someone was stealing U-25 from the plant and tampered with the files to cover the theft. Only she and Hillman knew about the theft, which was enough to build a nuclear bomb. Amy tells MacGyver that Hillman was going to take a copy of the report to Washington but died in the car accident, and she believes he was murdered.
Tim is working at the plant and remembering his high school days with Amy and MacGyver when the coroner calls to tell him that they've identified the body in the car and it wasn't Amy's.
MacGyver tries to comfort Amy and they share a tender kiss. They go to the nuclear plant to recover the hidden file. MacGyver figures the theft was an inside job and the thief must have hidden the U-235 somewhere in the plant. As they go in, a figure watches them from across the street. They go to the waste disposal chamber and recover the file, but Amy's pursuer locks them in the chamber and activates the waste disposal cycle. The door has a time lock which won't open for 60 minutes and the chamber will fill with radioactive waste in ten minutes.
Tim is at his station but talking with a security guard, Kyle, and doesn't notice that the chamber has been prematurely closed.
MacGyver opens up the time lock and applies an electrical circuit to accelerate the timing device. As he works, Tim finally notices the alert on his board and goes to investigate. MacGyver gets the door open just in time and they get out as the chamber fills with waste. Tim arrives and they show him the report and Amy tells him her suspicions. She and MacGyver suit up to check the storage chambers for the missing U-235. While Tim goes to call the regulatory agency, MacGyver and Amy go into the chamber. MacGyver finds several concrete-filled cylinders and discovers that the 235U is hidden inside of them.
As Amy and MacGyver come out of the chamber, they find Tim waiting for them… with a gun. MacGyver isn't totally surprised, since he'd figure that Tim might have been involved since he knew the plant so well. Tim explains that nobody was supposed to die but he and his partner had no choice once Amy discovered the missing material. MacGyver doesn't believe that his old friend can shoot him and simply walks away with Amy. Tim yells at them to stop but can't force himself to pull the trigger. They go to the control room but Tim's partner is waiting for them: Police Chief Train. Tim comes in and tries to convince his partner not to kill his friends, but Train warns that they know too much. Tim attacks him and in the struggle the gun goes off. Tim falls to the ground, mortally wounded. Train fires at Amy and MacGyver, who duck for cover behind the main console. The shots go wild, destroying the console and setting off a meltdown. Train runs for it while Amy confirms that the safety circuits are destroyed and they have no way to stop the meltdown.
MacGyver and the dying Tim figure that they can activate the coolant systems manually, but Amy will have to monitor the systems from the control room. MacGyver goes to the coolant system, but runs into Train, who is trying to escape with a concrete cylinder full of U-235. Tran chases after MacGyver, who doubles back and ambushes his pursuer. One of Train's shots goes wild, bursting open a pipe of radioactive material that sprays over him.
Tim and Amy have done what they can and Amy has come to look for MacGyver. She finds him as MacGyver gets Train into washdown to deal with the contamination. Amy takes Train's revolver and insists on going with MacGyver, warning he'll need her to wash him down as he activates the injection systems. They climb the coolant tower and MacGyver tries to open the valve. The wrench he's using slips and falls off the tower. With time running out, MacGyver comes up with a new tool: he removes the chamber from the revolver and uses it as a makeshift wrench. He gets the valve open and averts the meltdown. Tim, dying in the control room, sees that they've succeeded before he dies.
Later, MacGyver prepares to leave and Amy admits that she's happy she has him as a friend. They share a friendly kiss and hug before MacGyver drives away.