The Medellin Cartel kidnaps Alexander Shannon, a journalist and the son of a U.S. Congressman putting pressure on Columbian drug lords. Shannon is taken to a mountain drug camp and used as a hostage to force the U.S. to release an imprisoned drug lord. MacGyver smuggles himself into the camp within a crate being airlifted by helicopter. The camp foreman, Estebar, investigates the shipment but MacGyver hides beneath the packing. Once Estebar is gone, MacGyver slips away and makes contact with Shannon. However, Shannon has broken his leg, making escape off the mountain by climbing impossible. MacGyver goes to the mess tent and collects a motor and an exhaust blade. Meanwhile, he has Shannon bring him plastic garbage bags and bamboo scaffolding. Four hours later, Estebar notices something amiss and comes to investigate. MacGyver drops the side of the mess hall tent and flies away on the ultra-lite he's assembled, taking Shannon along with him.
Later, MacGyver gets back home and Pete is there to greet him. MacGyver says he's taking a break for the next month or so and after Pete leaves, he dozes off. Someone emerges from the shadows and heads toward the houseboat.
The next morning, MacGyver wakes up and discovers that someone has set his houseboat adrift. He goes outside and finds a woman waiting for him on a motorboat. She says that they used to be neighbors and he finally recognizes her as Zoe Ryan, a pesky next-door neighbor girl. She asks for his help and he refuses, but quickly reconsiders when she threatens to leave him adrift. She starts explaining about how her funding was cut and the university is against her, and finally gets around to asking him to help her find the Holy Grail.
MacGyver goes with Zoe to her college where she has a run-in with the football coach, Grogan, because she's having her students dig up the football field to excavate an Indian burial ground. The coach tells her to get the field restored by the upcoming game. Zoe takes MacGyver to her apartment but a man, Mammon, runs out, knocking MacGyver down. By the time MacGyver recovers, Mammon has escaped. They check Zoe's office and discover that Mammon was searching it.
Zoe finally explains that Erich Von Leer, a gem magnate, secretly used a grant to finance her last expedition to Greece. When she discovered he was responsible, Zoe refused to accept further funding from Von Leer so the college cut her project funding entirely. She smuggled back an artifact from Greece, Diana's Mirror, hidden in a souvenir pillow. The artifact was made by Ambrose, a 12th century alchemist.
Mammon goes to a limo and meets with Von Leer and his assistant, Shima Luca. He's confirmed Zoe's claim that the Temple of the Holy Rose exists and that it contains a giant ruby. He doesn't believe that the Temple also holds the secret to immortality, despite Shima's claims. Von Leer orders Shima to kill Mammon so Zoe and MacGyver can't trace him back to his organization.
Zoe takes MacGyver to see her mentor, Professor Wycliff, while explaining that the Temple of the Holy Rose allegedly contains the evidence Ambrose collected showing that Mankind lived in peace and harmony. Zoe hopes to find the Temple and share that knowledge with modern-day humanity so they can learn the same lesson. They meet Wycliff, who explains that the Temple contains the Cauldron of Regeneration, commonly known as the Holy Grail. He shows them Ambrose's papers at the university library, which show that the alchemist built the Temple of the Rose in a secret location. The key to finding the Temple lies in three of Ambrose's artifacts: Diana's Mirror, The Scepter of the Triple Deity, and the Holy Rose. The writing on the Mirror indicates that the Scepter can be found at an abbey in England. As they go over the papers, Zoe finds a reference to exorcising unclear spirits that MacGyver finds vaguely familiar. She asks MacGyver to go with her to London, admitting that Ambrose's inventive spirit is the same thing she admires in MacGyver. MacGyver gives in and accompanies her to London.
In London, MacGyver and Zoe stop briefly at their hotel, but Zoe insists that they go to the abbey immediately. She provides directions to the cabbie and they leave. However, Shima has been watching the hotel for their arrival and overhears the directions.
A mock torture chamber has been built inside Ambrose's abbey. The manager, Eunice, tells them that she's closing up, but MacGyver bribes her into letting them for ten minutes. Examining the main exhibit chamber, MacGyver remembers that he heard the phrase about exorcising unclean spirits at a baptism. They find the baptismal font and discover that Diana's Mirror fits into the basin. They place it into the basin and line up the markings, and three gem-tipped scepters extrude from the top of the font.
Eunice enters with Von Leer, Shima, and Von Leer's man Mammon and reveals that she's been working for the magnate all along. They prepare to kill MacGyver and force Zoe to lead them to the temple, but she places the scepters in the wheel of a rack and threatens to crush them. In response, Von Leer straps MacGyver to a sarcophagus and starts the water flowing from a nearby tank. The water hits a metal spoon attached to a ratchet on the pendulum, and the ratchet slowly lowers the pendulum blade. Left with no choice, Zoe surrenders the scepters. Von Leer's men take her prisoner, grab the scepters and Diana's Mirror, and depart, leaving MacGyver to a grisly death...