The pendulum continues to descend as the water from the tank slowly releases the ratchet. With time running out, MacGyver spots a shelf filled with fake decapitated heads. He manages to kick off his right shoe but fails to hit the shelf. With seconds remaining, MacGyver kicks off his shoe and hits a lever on a rack. The lever hits a suit of armor, and the knight's pike falls over and hits the shelf. One of the heads tumbles into the tank of water controlling the pendulum's descent. The water on the fake head blocks the outlet pipe on the tank. The pendulum starts to slice into MacGyver'e beltâ€¦ and then stops lowering.
The next morning, a startled cleaning lady finds MacGyver strapped to the sarcophagus. Once he's free, MacGyver goes to Von Leer's estate. As he arrives he spots Professor Wycliff, Zoe's mentor, arriving. As MacGyver slips over the wall, Wycliff confronts Von Leer and demands to know what he's done. Von Leer admits that he's holding Zoe prisoner and eliminated MacGyver, and warns Wycliff that he's fully implicated.
In her cell, Zoe receives an English breakfast from Eunice. Once Von Leer's henchwoman leaves, Zoe notices MacGyver outside, lowering a flag and taking it along with the rope. Avoiding a guard, MacGyver wraps the flag around a piece of outdoor piping. He then ties the rope to the bundle and tosses the bundle onto the battlements. Scaling the wall, MacGyver is forced to stop halfway when a guard passes beneath. Zoe distracts the man by throwing her breakfast onto the ground. Once the guard goes to investigate, MacGyver swings into the window and brings her up to speed. He warns that Wycliff is working with Von Leer and that they have to leave. Zoe refuses, insisting that they have to find the Temple of the Holy Rose. They escape to the rooftop, and MacGyver finds a chimney going to Von leer's study. He tells Zoe to stay put and climbs down.
In Von Leer's study, Wycliff is examining the writing on the Scepters and realizes that they indicate the Temple is somewhere in Europe. Von Leer notes that Shima believes the Temple holds the Philosopher's Stone which can grant eternal life. Wycliff doesn't believe it, and finds a reference to the â€œritual of the Rose.â€ MacGyver enters the rooms via the fireplace and tries to get the Scepters. Impatient, Von Leer threatens to torture Zoe over Wycliff's objections. He sends Eunice to get the girl. MacGyver heads for the door but Shima arrives and spots him. MacGyver knocks him out of the way and runs out of the room with the Mirror and the Scepters. Von Leer's men start searching the halls, unaware that MacGyver is hiding in a fireplace.
Unable to call out to Zoe above, MacGyver uses a bellows to shoot a model cannon's ammo up the chimney, catching Zoe's attention. She moves the rope to the new fireplace and lowers it to him. As MacGyver climbs up, Eunice realizes that Zoe has escaped to the ceiling. She goes there and spots MacGyver as he emerges from the chimney. As she prepares to shoot him, Zoe knocks her out with the pipe. They climb down and head for the outer wall as the guards give chase. They manage to escape in the rental car and pull off down the road. MacGyver wants to return to London but Zoe says that she believes the inscription indicates that the Temple is in Cherbourg, France. They can rent a plane at a nearby airstrip and beat Von Leer there. MacGyver finally gives in and they head for France.
Shima informs Von Leer that the prisoners have escaped. Wycliff reads the same notes that Zoe has and also concludes that the Temple is in Cherbourg. Von Leer departs for Cherbourg by helicopter with Wycliff, Shima, and Mammon.
As they travel across the English Channel, MacGyver warns that the knowledge in the temple that talks of Mankind's ability to co-exist may not be enough to change modern day Man's view of himself. Zoe remains undismayed and tries to figure out what the Ritual of the Rose is. They approach the Cherbourg ruin from the air and spot a ring of five rocks. The writing on the Scepters refers to the five petals of the rose and they realize the stones are the petals. They land and investigate the stones, and Zoe discovers a symbol and a cylindrical hole in the rock next to it. They discover that all three Scepters fit into the stone, providing two pivot points and a key. The rock swings up to reveal a golden casket. Inside it is a giant faceted ruby: the Holy Rose.
The inscriptions guide them to another rock, the Sacred Tree, with three more holes that the Scepters fit into. They realize the inscriptions refer to the sun, and instruct the reader to place Diana's Mirror and the Holy Rose on the stone in the indicated positions. MacGyver does so and the sun emerges from behind a cloud. The sunlight strikes the mirror and a beam is focused into the Holy Rose. As they look on, MacGyver explains that Ambrose discovered a light pump. The Holy Rose amplifies the sunlight and directs it through the gems on the three Scepters. The result is a laser beam, which strikes a nearby hillside. Gunpowder embedded in the rock by Ambrose ignites, blowing open the side of the hill. Inside is a collection of all of Ambrose's proof of his peaceful society as well as a golden miniature of the Temple of the Rose.
Von Leer arrives overhead as Wycliff finishes his translations. When the professor refuses to stand by and let Zoe die, Von Leer orders Shima to throw the professor to his death.
Remembering the inscriptions, MacGyver opens the top of the miniature Temple and finds a dish of red earth inside. Von Leer, Shima, and Mammon arrive and hold them at gunpoint. Von Leer has Shima take the red earth. However, the assassin reveals that he's a member of Society of Hashishim, and they've used Von Leer's resources to find the Philosopher's Stone and take it for themselves. Shima shoots Von Leer in the side and flees with the red earth, but Mammon shoots him. Von Leer goes after him and sends Mammon to kill Zoe and MacGyver. Using Zoe's camera flash, MacGyver blinds Mammon and then knocks him out.
Outside, the dying Shima collapses to his knees as Von Leer confront. The assassin refuses to let Von Leer triumph and lets the red earth drift on the wind before dying. MacGyver and Zoe run out and go to the Sacred Tree, and Von Leer ambushes them. As he prepares to kill them and then return to the cave to find the red earth's formula, MacGyver notices the clouds clearing above them. He tries to reason with Von Leer without success and then gets Zoe out of the way as the sunlight strikes Ambrose's light pump. The laser beam smashes Von Leer back into the cave and then brings it down around him and sealing the cavern for good.
As Zoe contemplates the dish with the red earth, she concludes that Ambrose would have wanted the cavern sealed away until the time is right, and Mankind isn't ready for his secrets. MacGyver wonders if Ambrose had something to do with the clouds clearing at just the right moment to save themâ€¦