The pendulum blade continues to descend as the water drips from the tank, knocking the ratchet loose and lowering the blade with each swing. Spotting a shelf of wax heads, MacGyver work off his right shoe and tries to kicks it... and misses. With one shoe left, MacGyver kicks off his left shoe and hits a lever, hitting a pike mounted on a suit of armor. The pike strikes the shelf, knocking a head into the tank of water controlling the pendulum. The hair on the head enters the outlet pipe, blocking the flow of water just in time. The blade eventually winds down and the next morning, a cleaning lady arrives and is surprised to find MacGyver there.
MacGyver goes to Von Leer's estate and slips into the manor after noticing Wycliff enter. The Professor goes to see Von Leer and demands to know what he's done with Zoe and MacGyver. He admits he doesn't like how Von Leer has altered their arrangement, but Von Leer insists he's been well paid and he's fully implicated.
Eunice takes a tray of food to Zoe, confined to a cell. Once Eunice leaves, Zoe spots a flag lowering from a flagpole outside. Peering out, she sees MacGyver lowering the rope and waves to him, warning him of a nearby guard. Once the guard moves on, Zoe signals the all clear and MacGyver finishes lowering the flag. He spreads it out and wraps it around an outdoor hose faucet. Taking the rope, MacGyver approaches the wall and uses the padded pipe as a grappling hook to climb the battlement. When the guard returns, MacGyver is forced to swing around the corner while trying to maintain his grip. Zoe tosses her tray of food off to the side to distract the guard so MacGyver can swing in through the window. He explains to Zoe that he saw Wycliff and he's implicated. MacGyver tries to get Zoe out but she insists on staying to find the Temple of the Holy Rose and he gives in.
While Wycliff works to translate the writing on the Scepters, MacGyver and Zoe climb to the roof and go the chimney leading down to Von Leer's study. He insists on going down on his own and starts descending. Below, Wycliff explains that one of the inscriptions directs the reader to a town in Europe and will take time to figure out where it is. However, he disagrees with Shima's insistence that Ambrose created the Philosopher's Stone, which will grant eternal life. As Wycliff reads a passage concerning the "Ritual of the Rose," MacGyver sneaks out of the fireplace and grabs the Scepters. When Von Leer threatens to torture Zoe for the information, Wycliff balks and Von Leer points out that Zoe will have figured out he's involved by now. MacGyver tries to sneak out but Eunice arrives, blocking his path. Von Leer tells her to bring Zoe and Shima. Once she's gone, MacGyver crawls back to the fireplace but Shima arrives and spots him. MacGyver knocks him down and runs out with the artifacts. As Shima orders his men to search, he's unaware that MacGyver's hiding nearby in a fireplace.
MacGyver grabs a fireplace bellows and fires a cannonball from a miniature camera up the chimney to signal Zoe. Below, Eunice discovers that Zoe has escaped and realizes she's gone to the roof. Meanwhile, Zoe drops the rope to MacGyver so he can climb up. Eunice comes up and doesn't find Zoe. MacGyver climbs up the chimney and Eunice prepares to shoot him, but Zoe knocks her out with the iron pipe. MacGyver and Zoe climb down but as they flee the grounds, the guards spot them and open fire. They get over the wall and escape by car. MacGyver is ready to go back to London and notes that Wycliff was stuck, but Zoe figures out he'll figure it out soon enough. She knows that the inscription refers to Cherbourg, France, and there's a nearby airstrip where they can charter a private flight. MacGyver finally gives in completely and they head for the airfield.
Shima reports that Zoe and MacGyver have escaped, and Wycliff realizes that the Scepter refers to Cherbourg. They depart for France via helicopter.
En route, Zoe figures out where the ruin is but has no idea what the Ritual of the Rose refers to. MacGyver warns her that she might be disappointed if she isn't able to change the world the way she hopes she can with the knowledge in the Temple. They spot the ruin from the air and a nearby ring of rocks that aren't indigenous to the area. Ambrose referred to five petals on the Holy Rose, and there's five stones. They land and investigate the area, and Zoe spots a circular symbol from one of the Scepters. They insert the matching symbol into the hole and discover it's a perfect match. There are similar markings for the other two Scepters and they insert the artifacts in accordingly. MacGyver realizes the first two Scepters work as pivot points and the third one as a key. The top part of the stone opens to reveal a golden casket holding the Holy Rose. Zoe opens it and finds an enormous ruby.
The next step is to look for the sacred stone holding the key to the temple. Zoe finds the rock and reads the inscriptions on it. MacGyver has found more holes and inserts the three Scepters into them. They form a straight line but nothing happens. The inscriptions say to rest Diana's Mirror on the Sacred Tree, and the power of the Trinity will give the earth a new beginning. The inscription refers to the sun and MacGyver realizes that the stone is the sacred tree. He places Diana's Mirror on the top. When the sun comes out from behind a cloud, the Mirror focuses the mirror through the ruby, which pumps the light through the lenses on the Scepters. The result is a ruby laser, focused on a nearby mountain. The laser beam blasts open the rock, and MacGyver realizes that Ambrose embedded the rock with gunpowder. Inside is a cavern holding a miniature of the Temple of the Rose and artifacts representing Ambrose's peaceful society.
Wycliff duplicates Zoe's conclusions and Von Leer arrives above the stone. When Wycliff refuses to participate in Zoe's death, Von Leer has Shima throws the professor to his death.
MacGyver realizes that the Holy Grail is hidden beneath the miniature Temple. He opens it and finds a dish containing a red powder. Von Leer, Shima, and Mammon arrive and Shima take the red earth. Shima reveals he's part of the Society of Hashishim and they've used Von Leer's resources. However, they no longer need Von Leer. Shima shoots and wounds him and Mammon shoots Shima, driving him off. Von Leer goes after Shima and tells Mammon to dispose of Zoe and MacGyver. Mortally wounded, Shima pours out the red earth and lets it disperse on the wind with his last breath.
Inside the cavern, Mammon stalks MacGyver and Zoe. MacGyver uses the timer flash on Zoe's attachment to first attract his attention and then blind him, and finally knocks him out. The two run outside and the wounded Von Leer surprises them. As Von Leer rambles on about his plan to find the formula for the red earth within the temple, MacGyver sees the clouds clearing above. He tries to explain that there's no formula and Ambrose built a museum for the fortune. Von Leer doesn't believe him. The sun comes out, reactivating Ambrose's laser assembly. The beam knocks Von Leer back into the cavern and then brings it down upon him, sealing it away forever. Zoe picks up the dish holding the red earth and believes that Ambrose wanted the cavern sealed until the time the peoples of the world are ready for it. MacGyver figures that the red earth is just dust, and that the cloud clearing at the right moment means someone was on their side.