At the Westport nuclear processing plant, Director of Research Amy Austin gets a call from the state police about her general manager, Gerald Hillman. They inform her that his car went off the road and he died in the accident. Amy is unaware that someone is watching her from a door. She then goes to the files and checks the report she made about missing U-235, which she copied to Hillman. She then tries to call out, unaware that a figure in a protective suit has cut off the line. Amy gives up and then runs out the door as the figure comes after her. She runs through the plant and hides the file behind a pipe in the waste disposal chamber, then hides in the chamber. The figure passes by her and she runs to a phone and calls... MacGyver.
MacGyver is at home playing table hockey with his friend and wins. Susan challenges him to another game and as they play, the answering machine picks up the call. MacGyver takes it immediately and she says that she's in trouble and needs him. MacGyver says he'll be there tomorrow and Amy says her friend died and someone is trying to kill her. She wonders if she has the right to involve him and MacGyver assures her he'll be there. Amy says to meet her at "their beach," but the figure sees her and she runs away.
The next day, MacGyver arrives at Westport Beach and goes to the their special spot as he remembers that he moved on and Amy stayed. He remembers back to when he met with Amy and set it up so that the two of them could take a freighter to the Mediterranean. Amy is taken aback and says that the future lies with the nearby nuclear processing plant. She didn't think MacGyver was serious when he talked about traveling. She sadly drives off without him.
In the present, Amy drives up into the nearby parking lot and honks at him. MacGyver waves... and then looks on in horror as the car blows up. Later, MacGyver goes over the car as his old friend Tim Wexler arrives. Tim worked at the plant as well and MacGyver explains he was there and doesn't think it was an accident. The police chief, Ed Train, notes that Amy's parents died in a plane crash a year ago and her boss Hillman died the previous night. MacGyver gives him a piece of the gas tank and points out that there's a hole indicating someone used an explosive bullet. Then he asks if Amy was close to anyone else but Tim confirms that nobody else is around. Train mentions when the funeral will be and MacGyver insists on being there.
After the funeral, he gets in his car and discovers that Amy is still alive, and hiding in the backseat. She tells him to drive to her father's place. She explains that she sent her roommate to get MacGyver and the murderer mistook her for Amy. Amy breaks into tears and MacGyver tries to comfort her. Amy explains that someone tampered with the files to cover the fact they stole enough U-235 to make a nuclear bomb. Only Amy and Hillman knew about the theft. They go inside as Amy explains that Hillman was going to Washington with a copy of the records when his car went off the road. Amy figures someone killed Hillman.
At the nuclear plant, Tim is going over yearbook photos of himself, Amy, and MacGyver when he gets a call that the coroner has confirmed Amy didn't die in the car explosion.
At the house, Amy and MacGyver kiss and she thanks him for coming. MacGyver figures someone at the plant stole the U-235 and they need to recover the hidden audit report. They drive to the plant, which is almost empty on a Sunday. They go in, unaware that someone is outside in a car watching them.
MacGyver figures the U-235 is still hidden in the plant. Amy leads MacGyver to the waste disposal chamber and gets the report. The suited figure seals the door and Amy warns that the door is on a 60-minute time lock. The disposal hatch opens and Amy warns they only have ten minutes before it becomes too hot to breathe. Tim and the security guard, Kyle, are busy and don't notice the warning lights. MacGyver goes to the door and opens the lock up, then rewires it to accelerate the time clock with an electrical surge. In the control room, Tim finally notices someone has activated the manual override on the waste disposal door. In the chamber, MacGyver gets the door open and they get out just as Tim arrives.
MacGyver and Amy show Tim the report and suit up to check out the storage chambers and find the missing U-235. They tell Tim to call the regulatory agency and equip themselves with radiation badges. They go through the containers and MacGyver figures the thieves stored the high-grade U-235 in with other high-grade material. He finds some spare cylinders filled with concrete and discovers that the stolen U-235 is inside of it. As they emerge, Tim is waiting for them with a gun. MacGyver isn't surprised: he already figured it was an inside job and Tim had the necessary experience. Tim regrets the deaths but he's in too deep now. MacGyver doesn't believe that he'll shoot and walks away with Amy. Tim follows them and points the gun, but they keep walking and he can't bring himself to pull the trigger.
In the control room, they try to get Kyle to help, but Tim's co-conspirator is waiting for them: Train. Tim tries to convince him not to shoot them and they struggle for the gun. Tim is shot in the side and MacGyver and Amy duck for cover as Train opens fire, hitting the control panel. Train runs as Amy realizes that the reactor is going into meltdown because the coolant is shut down. Tim warns there's nothing he can do but MacGyver tells them to go. He plans to open the injection system manually despite the risks. MacGyver goes to the injection system, while Train removes the stolen U-235. He opens fire on MacGyver and then chases after him. Tim and Amy set up the injection system and tells Amy to go help MacGyver.
As he chases after MacGyver, Train tries to justify his theft figuring his buyers will never use it to make a bomb. MacGyver manages to ambush Train, knocking him into a wall as he shoots a nearby pipe. As Amy arrives and picks up his revolver, Train is badly contaminated and they put him into washdown. In the control room, Tim tells Kyle to leave and that it's too late for him.
Amy insists on going with MacGyver, pointing out he'll need her to wash him down as he opens the injection system. They climb up to the top of the tower and Amy hoses MacGyver down as he tries to open the injection system with a wrench. He drops it trying to open the valve and is unable to open it by hand. He removes the cylinder from Train's revolver and uses the resulting gap as a makeshift wrench to open the injection system. They abort the meltdown and embrace. Tim, dying at the controls, lives long enough to see that his friends have succeeded.
Later, Amy admits that MacGyver has stored up a lot of memories. She's happy that she has him as a friend and they exchange a friendly kiss on the cheek before MacGyver drives away.