Five Years Earlier
MacGyver and his college mentor, Professor Atticus, are exploring the Thera ruins of Greece. Atticus finds a gold medallion which the inscription Atlantis Anaduotai: "Atlantis Rises." After taking a photo, MacGyver realizes the medallion's mount is a pressure switch. Using a pressure cap, MacGyver maintains the pressure and removes the medallion. When Atticus looks around, he accidentally sets off a trap and MacGyver pulls him out of the way just in time as the released spear skewers the lens cap. They set off a backup trap and the exits seal shut and gravel starts pouring into the room. The room fills up to almost the very top before the flow of gravel stops, and the two men try to figure a way out.
In London, Atticus is giving a presentation to the Royal Academy of Archaeological Science about the city of Atlantis. He lectures them on how the Atlanteans built a great city on a volcano and worshipped an as-yet-unidentified object, the Torch of Truth. After the volcano erupted and the city was destroyed, the few survivors hid the Torch in the Tower of Fear, and wrote their story on pages of platinum and placed them in a book. In 950 B.C., Solon, a Greek scholar, found the book and the Torch, and created an Ark to store the Torch. Solon then gave his disciples the book and left in search of Atlantis, and disappeared from the annals of history.
Atticus explains that he found the medallion, the key to finding the missing Ark. He wants the Royal Academy to find an expedition for him to trace Solon's path and find the relics, which will lead to Atlantis. The Academy director tells hi that the key will stay in the academy collection and they have no intention of funding any wild goose chase. They dismiss Atticus and warn that they will be reconsidering his tenure.
Several Months Later
MacGyver and Atticus travel to the Balkan Peninsula and evade the soldiers at a local military base. Beneath the base are ancient ruins. As they slip into the catacombs, Atticus explains that Solon's disciples fled Greece, traveled to England, and formed the Cult of Solon. The Romans eventually hunted them down, forcing them to the Balkans. As they enter the ruins, the two men are unaware that a soldier has discovered their footprints and summoned his superior, Colonel Petrovic.
In the catacombs, MacGyver finds a skull bearing the sign of Solon. When they turn it, a hidden panel opens to reveal the Ark of Solon. The inscriptions speak of taking the Torch to the Temple of the Ages to reveal the lost treasure of Atlantis. Before they can remove the Ark and escape, Petrovic and his men arrive and arrest them. He takes them to the base and beats MacGyver, telling him to confess that he's a spy. MacGyver insists that the area is under a UN ceasefire but Petrovic says that he's there to conduct ethnic cleansing. MacGyver briefly tires to attack him but is easily knocked down. Petrovic activates a large section of electrified flooring in front of the door and leaves with the Ark and MacGyver's Swiss Army knife.
Once Petrovic leaves, MacGyver reveals to Atticus that he secretly took the colonel's cigarette lighter. He balances across the wooden chair on the floor so he can lean over and use the flame from the lighter to heat the lock. As he works, Atticus sheepishly admits that he lost his tenure and that he's financing the "expedition" on his own. Once the lock is properly heated, MacGyver swings a light bulb on a cord across the floor. The heat causes the bulb to explode and ignite the filament. When a guard comes in, they feign unconsciousness to lure him closer, and then use a chain to swing the door into him and knock him out. MacGyver uses the spring action from the soldier's rifle to open their manacles and then they slip outside and find a tent with clothing they can use to disguise themselves.
Once Petrovic leaves his office, MacGyver and Atticus sneak in to recover the Ark. They find an old scratch and MacGyver discovers that it is magnetic. They hide the Ark beneath a coat and head for the gate, but are forced to retreat into a storage depot when soldiers arrive. There's an old jeep inside but it's missing an engine. Petrovic discovers the prisoners have escaped and sounds the alarm. MacGyver locks the depot's door and attaches two LAW rockets to the back of the jeep. As Petrovic and his men try to break down the door, MacGyver rigs up a grenade to the rest of the stored weapons, and then gets into the jeep with Atticus. When Petrovic's men break down the door, MacGyver triggers the rockets, which propel the jeep forward through the men and toward the gate. Using another LAW rocket, MacGyver blasts open the gate and they escape.
MacGyver and Atticus go back to England and MacGyver meets with Kelly Carson, a science professor at the academy who is just finishing a lecture. MacGyver asks for her help but she's reluctant to help him. MacGyver explains that thy found the Ark by ignoring the Academy. He provides Kelly with a sample and she agrees to analyze it, but warns that her grandfather, Professor Simon Carson, still holds a grudge against Atticus. Simon arrives from Greece and apologizes for missing Kelly's lecture, and then dismisses Atticus' find. He begrudgingly says he'll look at it later before he goes back to Greece.
After her grandfather leaves, Kelly explains that Simon came to England to convince her to accept tenure. They go to her lab and Kelly runs the test while explaining that Simon wants to keep her safe at the university, but she finally admits that she wants to get out and see the world. MacGyver encourages her to leave but Kelly explains that she doesn't want to disappoint her grandfather, who raised her after her parents died. As she finishes the analysis, she admits that she had a crush on MacGyver when they were in college together. She avoids saying more by focusing on the analysis, which shows that the Ark was forged in 600 B.C. There's a scratch on it that has traces of tin, found in Exeter, Cornwall. MacGyver goes to tell Atticus and Kelly insists on going with him to where the Ark and medallion are being kept at the Academy.
As they cross the grounds, Kelly admits that Simon is a conservative who doesn't want to have to rewrite the history books. As they enter the academy building, a man posing as a janitor calls a Lord Cleeve on the radio. Cleeve tells the man what to do next.
Simon arrives and insists that the medallion and the Ark have no connection. Atticus points out that the same riddle on the medallion is also inscribed on the Ark. There are also symbols representing the Greek gods, including Hecate, the demon of the night. Simon dismisses Atticus' theories and the Academy director arrives. He's talked with the Balkan government, who claim the Ark is a national treasure and want it returned. The director takes out the medallion and MacGyver notices that it's magnetized. Atticus takes it and attaches it to the Ark, opening a panel. However, there's nothing inside. Atticus wants to take the Ark to Thera to prove his theories but Simon and the director refuses. Kelly finally has enough and tells her grandfather that she's going to help Atticus and MacGyver find Atlantis. Simon accuses her of betraying him and blames MacGyver and Atticus of turning her against him. As he leaves, the director tells Atticus that he's to clean out his office and leave.
As they go, MacGyver speculates that the Cult of Solon kept the Torch in the Ark, but removed it and took it with them. Cleeve's man listens in and then slips in and shoots the director with a tranquilizer dart. The director manages to set off the security alarm before he collapses. MacGyver and Atticus hear it and go back, and find the thief taking the Ark. MacGyver tackles the man, who drops the medallion. He slams MacGyver into a display case and runs away. Atticus secretly pockets the medallion while MacGyver goes after the man as he escapes in a stolen cab. He chases the thief to the Thames but the man escapes in a boat.
MacGyver returns to the academy display hall, where Inspector Rhodes of Scotland Yard is investigating the theft. He confirms the thief is Yannis Zavros, a former military officer who now leads a cult of fanatics who believe they're the descendents of Alexander the Great. Zavros and his people plan to take back Macedonia for their own. They steal and sell artifacts on the black market to fund their operations, and are rumored to work with Lord Cyril Cleeve. Atticus recognizes Cleeve's name and remembers him as a student who bought his title and purchased an estate in Plymouth. Rhodes admits that he has nothing conclusive on Cleeve and that if he is involved, he already would have smuggled the Ark and the medallion out of the country to sell overseas.
Once he realizes that the inspector didn't find the medallion, MacGyver figures that Atticus took it and demands answers. Atticus admits he pocketed the amulet and takes MacGyver and Kelly to his office. He explains that Cleeve stole the Ark to gain access to the inscription and use it to find Solon's treasure. Atticus tells them that according to the riddle, the inscriptions to the gods describe an alignment that will take place in two days' time, and they have that long to find the Temple and the Ark. In Greek, "Tower of Fear" translates as "Thera," and Atticus believes the Temple is near there. As he goes through his files, Atticus finds a photo of himself and Simon at Thera, near the volcano. He believes that before the Cult of Solon fled England, they hid the Torch of Truth in the caves at Exeter.
The trio travels to Exeter and enters the ancient caves. Inside they find inscriptions left by the cult talking about Atlantis. MacGyver figures that the cult hid it the book where only Solon could find it. Inside the cave is an altar with a metallic hoop, and MacGyver realizes that the chamber was built as a second giant-sized Arc. He places the medallion in the center of the hoop and it hangs there, caught in the magnetic fields. The hoop then turns and a rock wall opens to reveal the Torch of Truth: a golden staff with a crystal headpiece. MacGyver carefully enters the chamber and notices stalactites mounted in the ceiling. He suspects a trap, but when he removes the staff, nothing happens. However, as he starts to leave, Cleeve and Zavros arrive. Lord Cleeve tells MacGyver to hand the staff over to his partner... Atticus.
The criminals tie up MacGyver and Kelly and put them in the torch chamber. Atticus protests, insists that their arrangement didn't include killings. Cleeve reassures him but once the professor leaves, Zavros seals the chamber. As the rock wall starts to close, the stalactites start shooting down from the ceiling. MacGyver uses one to cut their ropes and they slip through the chamber door just before it closes. MacGyver takes a moment to regret the fact that Atticus has betrayed them, and then they figure that Cleeve will take the Torch to his estate. They go there and sneak onto the ground, and spot Zavros preparing a plane for departure.
MacGyver has Kelly stay outside while he slips into the manor and makes his way to the study. He listens as Cleeve boasts to Atticus that he soon will find Atlantis and obtain the treasure, buying his way into the history books as an archaeologist. Atticus objects but Cleeve dismisses his protests. Meanwhile, Kelly approaches the plane and takes the ignition key out. She throws it into the field to stop Cleeve from leaving. However, Zavros returns and captures her as she tries to call for help on the plane's radio.
MacGyver listens as Atticus complains that he was forced to turn to Cleeve for help when the academy refuses to back his expedition. Zavros brings in Kelly and Cleeve figures that MacGyver must be nearby. While Kelly refuses to answer their questions and stalls for time, MacGyver rigs a candle and string to a mounted suit of armor holding a mace. He positions the mace above a table holding china plates. He lights the camera and then walks into the study before Zavros can start beating Kelly for information. MacGyver informs Atticus that Cleeve tried to kill them, and that they've summoned the police. When the candle burns through the rope, the mace falls on the china. Distracted, Zavros turns and MacGyver knocks the gun out of his hand. As they escape, Atticus stops Zavros from getting his gun back and goes after the others, and tells MacGyver that he's on their side.
They go to the plane and try to start it, and Kelly sheepishly admits she threw away the key. MacGyver rigs the ignition using his Swiss Army knife and they fly away before Cleeve and Zavros can stop them. As they leave, Atticus apologizes for turning to Cleeve, but admits he was desperate, He believed that he could control Cleeve, and hopes to use the knowledge of Atlantis to show that the ancient peoples could live in peace and harmony. Atticus hopes that the information can inspire people in the present to do the same. As they fly to Greece, MacGyver warns that Cleeve and Zavros will follow them.
The trio lands near Thera and take a jeep to the site where Simon is working. They discover that Cleeve and Zavros beat them there and have knocked out Simon. They call in a doctor to treat Simon for his concussion. Kelly discovers that Cleeve has taken her grandfather's maps and charts, and they have less than 12 hours before the planetary alignment. Simon brought the Ark with him, and MacGyver notices that the lid is not magnetic, unlike the rest of the case. MacGyver cuts open the lid and discovers a secret compartment holding one of the platinum pages, riddled with holes.
Kelly leads them to the volcano and they find the caves leading into the temple. The entire structure is built on top of fumaroles channeling heat from deep beneath the surface. They find a tunnel and go inside, to discover the temple with a model of the solar system. The solar model predates Copernicus' discover by thousands of years. A vent in the ceiling shows the sky, and the planets moving into alignment. As they draw closer in alignment above the volcano, the increased gravitational force is destabilizing the volcano. The trio searches and finds a door with the mark of Hades. Opening it, they find a passageway with gas jets... and Zavros' burnt corpse. Cleeve enters and holds them at gunpoint, and explains that Zavros betrayed him and tried to get the treasure first. He tells MacGyver to deactivate the fire trap or he'll kill Atticus and Kelly. MacGyver examines the model and realizes that the riddle refers to the planets in alignment. He also finds a slot in the base that fits the platinum page from the Ark. Inserting the page unlocks the model and aligns the miniature planets, deactivating the gas jets. As they go on, Kelly notices that there's an unknown red planet mounted within the model.
Cleeve forces his prisoners through the passageway into the cavern beyond. Inside is a flaming lake and a set of vault doors mounted into the wall. Above them is a massive hole in the side of the volcano, which reveals the planets moving into alignment above them. Finally they find a macabre relic: Solon himself, frozen in hot ash and lava at the moment that the volcano exploded when it destroyed Atlantis. The statue holds the platinum book in its arms and Cleeve yanks it free.
The planets are close to alignment but nothing happens. They realize that Hecate, mentioned in the inscription, has yet to appear. As they look up, the "red planet" appears and MacGyver realizes that the red planet in the model represents a meteor. Its gravitational force completes the combination and the temple doors open. Inside is an altar with more page slots and three urns. MacGyver takes the book from Cleeve so he can solve Solon's riddle. As he takes the pages out of the book, MacGyver explains that Solon created the world's first computer, powered by the volcano's heat. The pages are crude punch cards. MacGyver places each one in the properly marked slot and then inserts the Torch into a socket on the altar. Pulling it causes the crude steam engine to raise a platform in the middle of the flaming lake to rise up. Atop it are watertight treasure chests.
Cleeve runs out onto the platform and opens the chests, but discovers that there is no gold or jewels. The only thing inside are scrolls. He tears them apart to find the treasure beneath, but MacGyver and Atticus realize that the scrolls are the treasure: Atlantis' combined knowledge. Atticus attacks Cleeve to stop him from destroying the scrolls but the black marketer shoves him aside. MacGyver tackle the man and knocks him into the flaming lake.
As they prepare to leave, the planetary alignment sets off the volcano and collapses the tunnel out. With only a few minutes remaining until eruption, MacGyver shuts down the steam engine and tells Atticus to use his jacket to block one of the exhaust pipes. He finds a funnel-shaped piece of metal, attaches a rope to it, and places it over the second vent. He then tells Kelly to pull the lever and reactivate the steam engine. The steam pressure shoots the funnel up through the hotel where it hooks on the rocks above. Tying the rope off into a loop, they use the steam engine to create a hoist. Kelly and Atticus make it up, but MacGyver is trapped halfway up. He climbs the rest of the way up and the others pull him over the edge as the temple explodes into flames. Kelly kisses him in relief and they watch as the knowledge of Atlantis is destroyed.
Later, a triumphant Atticus gives a lecture on the advanced civilization of Atlantis to a group of schoolchildren. In the back, MacGyver, Kelly, and Simon look on.