As a local emir predicts his arrival, MacGyver parachutes into the country of Kabustan and tracks down a downed airplane. It belongs to Jack Dalton, who MacGyver soon locates. Jack, unconcerned, explains that he's there on legitimate business for the Phoenix Foundation. MacGyver isn't so sure and wonders how Jack convinced the Foundation to underwrite his latest scheme. Jack insists that it isn't a scheme, and that he has actually found the Fountain of Youth in nearby Amakash Valley. MacGyver figures that the elderly Foundation is interested in anything that can make them younger. Jack insists his intentions are honorable, and points out that his eye isn't twitching. MacGyver warns that the rescue helicopter will be there in four hours, then goes with Jack to collect some water samples.
Jack explains that they need to get permission from Baba, the local emir, to visit the Fountain. En route they meet Mukti, a young girl who is waiting for MacGyver. She informs them that Baba has finally considered giving Jack permission to visit the spring, and that MacGyver is also allowed. Jack points out that Mukti is actually 42 years old but appears much younger due to the Fountain's waters. As they go to the temple, Mukti explains that her people exist apart from the Kabustani government and govern the area themselves without outside interference. She's also happy that Jack has offered to take her with him.
At the temple, Baba asks Jack why he wants the water. When Jack tries to lie, he finds himself mesmerized into speechlessness. MacGyver explains that they want to take a sample and Baba looks deep into his eyes, and then gives them permission. As the two men leave, Baba's assistant Ram is unsure but Baba explains that MacGyver is prophesied to assist them.
Mukti takes them to the Fountain and Jack starts talking about rights, raising MacGyver's suspicions. The earth shakes and Mukti notes that some who have visited the Fountain have never returned. The Fountain suddenly stops and Mukti explains that it has never done that before. MacGyver figures it's not a natural phenomenon and they head upstream to investigate. They're unaware that Baba and Ram are following them. Baba insists that Mukti should accompany them, as it is her destiny as well.
Upstream, the trio finds a pump house guarded by Kabustani soldiers. A squad of soldiers led by Captain Samad spot them and prepares to open fire. Samad orders his men to spare Mukti. Baba steps out and takes the first bullet. MacGyver and the others get him to cover and take refuge in a nearby meditation cave. Baba tells MacGyver that he should continue on his quest and take Jack and Mukti with him. He insists that his wound is a minor one and that Ram will attend to him.
They return to the pump house and MacGyver puts the radio transceiver from Jack's plane into the water supply. Using a radio tracker, they follow the signal to its source: a mountain base. After drawing off the guards, they sneak in and discover that the base is a heavy water plant used to manufacture fissionable materials for H-bombs. They spot Dr. Liang, a Chinese expert in nuclear weapons who is acting as an advisor to the Kabustani government. MacGyver goes to get proof and sneaks into a control room, and then steals a video tape from the security cameras. Jack gets bored and finds some water samples in test tubes. However, Captain Samad spots him and follows him. Jack and MacGyver both return to Mukti, but Samad closes in to capture them. MacGyver manages to hide the videotape in a garbage can before they can search him. Samad looks at Mukti regretfully and tells him that she should never have come there. He finds a contract from the Be Young Company on Jack and figures it's a cover for their spy operations. When he finds a letter from the well-known Phoenix Foundation, Samad believes that confirms his suspicions and has them locked up as spies.
As they wait for Samad to deal with them, MacGyver forces Jack to explain that he's working with the Be Young Company and they're paying him $200,000 to get the rights to the Fountain from the Amakash villagers. MacGyver comes up with an escape plan and tells Jack to give him the one test tube that he certainly hid somewhere on his person. Jack gives up the sample and MacGyver breaks the test tube, and then uses a piece of glass to cut through the cell door's wiring. He then places the tube stopper in the door to jam it the next time it closes.
Samad and Liang return, having realized that a videotape is missing. MacGyver refuses to reveal where he hid it and Liang orders their execution. Samad tells Mukti that he can't do anything for her even though she once saved his life. Once they're alone again, Mukti explains that the much older Samad is actually her twin brother and grew up in Amakash with her. He turned to violence and the villagers were prepared to execute him, but Mukti convinced them to merely exile Samad instead.
Once they're sure Samad and Liang are gone, MacGyver opens the cell door and then recovers the videotape. They head for the exit as Samad discovers that they've escape. The trio burst through the gates and knock out the guards using a ladder, then head for the pump house. MacGyver tells Jack to get the videotape to the UN while he stays behind to delay Samad. As Jack and Mukti flee, MacGyver closes the pump valves and gets clear. The water pressure breaks up and the pump house explodes just as Samad and his men arrive. The soldiers are stunned and MacGyver makes good his escape.
Later, the group meets at the temple where Baba has recovered. The helicopter arrives but Mukti says that she'll be staying in Amakash, having realized that her place is in the valley. As MacGyver and Jack leave, Ram wonders if Jack will invite more outsiders in. Baba assures him that Jack's plans will change. Sure enough, Jack decides that revealing the Fountain to the outside world would ruin the perfection of the valley. He dumps all of the water… except for one dose which he drinks himself.