MacGyver volunteers to fly into a satellite crash zone via helicopter when a Phoenix space satellite crashes down in the middle of a sheep ranch. Pete and the government representative, Colonel Phelps, monitor him from a defense bunker. MacGyver dons a protective suit with a mounted camera and proceeds into the crash zone. The rancher has been evacuated to safety where he's telling the press that something is going on and the military is responsible. While the military representative denies reports of chemical warfare, Pete wonders if the person responsible, Dr. Sandra Millhouse, is watching. Millhouse sent a plant accelerant into orbit aboard the Phoenix satellite without authorization. The satellite has crashed to Earth and MacGyver has to recover the sample in the next 42 minutes, or the military will launch a napalm strike to sterilize the area.
As MacGyver proceeds into the crash zone, he finds over 900 dead sheep. Worse, all of the animals in the area have died, apparently within minutes and with no warning. Military jets fly overhead and Pete demands that Phelps pull them back and give MacGyver the time he needs to complete the mission. Phelps reluctantly orders them further back from the crash zone. MacGyver finally locates the satellite on a spit of land extending into a lake. As he approaches it, he slips down a slope and is knocked unconscious. Pete and Phelps lose the signal and the colonel concludes that the organism has killed MacGyver as well. He calls in the air strike over Pete's objections.
MacGyver wakes up and discovers that although his suit is intact, the radio antenna was damaged in the fall. He can hear Pete and Phelps talking but can't communicate back. Pete tells MacGyver to get out if he can but MacGyver makes a run for the satellite. As the jets close in, MacGyver pulls out the transmitter dish from the satellite and hooks it up to his camera. Pete and Phelps see him just in time and Phelps orders the jets to abort. MacGyver extracts the sample cylinder, contains it, and calls for extraction.
Pete and Colonel Phelps go to a Phoenix Foundation facility six stories beneath the earth. All but essential staff have been given the weekend off. Pete tries to find Millhouse and comes across her puppy, Ace. He finally finds her in the hydroponics lab and expresses his displeasure with the fact she hid the plant accelerant aboard the satellite. He notes that this isn't the first time she's violated procedure. Millhouse insists she did what she had to, to bypass the bureaucratic red tape and that Pete needs to give her time to confirm her experiment was a success. Pete tells her it's over. MacGyver arrives and sends the sample down, then goes through decontamination. Phelps meets him and apologizes for calling in the air strike, but MacGyver says he understands.
Millhouse and Pete are examining the mutated sample in a containment chamber when MacGyver arrives. She wants to expose a white lab rat to it but he says he's seen enough dead animals for one day. She agrees and MacGyver informs her that the cylinder holding the sample was cracked. Millhouse runs a scan and notes that the mutated organism is getting stronger. Phelps brings in the autopsy report: all of the animals died of old age. Millhouse argues that the mutated plant accelerant, properly controlled, could accelerate crop growth and put an end to world hunger. Pete refuses to cover up the problems or make excuses to the government. Millhouse shows MacGyver her hydroponics experiments: plants that can survive in any Earth environment and withstand high levels of pollution. MacGyver is impressed but says there's a right way and a wrong way. Millhouse says it's results that count.
Pete returns to inform her that the government has ordered him to destroy the mutated organism. Millhouse starts to argue but they're interrupted when an integrity seal alert goes off. The organism has mutated and is starting to eat through the window seal of the containment lab. They have seven minutes to restore containment integrity or the self-destruct will go off to prevent contamination. MacGyver has Millhouse train a Bunsen burner flame on the dissolving seal while he extracts a freon gas cylinder from a refrigerator unit. Once the sealant has melted and filled in the gaps, MacGyver uses the freon to freeze it in place and restore integrity.
Millhouse has no choice but to given in and destroy the mutated organism, using a remote laser. She then places a lab rat in the chamber and confirms that it's been eradicated. Phelps leaves for Washington to give a report and Millhouse tells MacGyver and Pete to get the hell out of her lab. MacGyver says that he understands the need for experimentation but in this case the risks are too great. Millhouse shows him her computer disks holding all of her research. MacGyver tries to comfort her with the knowledge they'll come up with a solution eventually.
Up top, MacGyver and Pete prepare to leave and Pete tells MacGyver about the time Millhouse tired to smuggle a Dutch elm tree additive out in a dog's bladder. He admits that she never gives up, and both men realize Millhouse gave up too easily. As they head back down, Millhouse goes to the hydroponics lab and removes a hidden sample from a containment unit. When MacGyver arrives, she seals the room and admits that she figured someone would order her to destroy the main sample. She insists that everything is safe, but her puppy Ace leaps at her and knocks the sample to the ground.
The integrity alarm goes off and MacGyver and Millhouse look on as Ace starts to age. He crawls over to Millhouse as she starts to show symptoms of aging and collapses to the floor. Pete arrives and MacGyver tries to find a containment suit but it's too late: Millhouse is now all but dead of old age. She apologizes to Ace, who dies in her arms, and thanks them for trying. The plants in the hydroponics lab are aging as the organism mutates again. MacGyver gets her diskettes and promises Millhouse he'll get them to safety, and she lives just long enough to hear him.
With five minutes left to self-destruct, the hallway isolation doors start closing off the hallways. Pete and MacGyver manage to get past them and open the elevator doors. However, the containment protocols automatically shut down the elevator. They get up on the roof and try to use the maintenance override, but it only moves the cab up a few inches at a time. Realizing they'll never make it in time, MacGyver goes to one of the doors and removes the transformer. He hooks it up to the maintenance override and boosts the power. They move up the shaft and get to the top just as the self-destruct goes off. They get clear as an enormous explosion brings down the entire laboratory. They can only express regret at the loss of life.