In the Thera Ruins of Greece, MacGyver and Professor Atticus enter a chamber and Finch finds a gold medallion mounted in an alcove which says Atlantis Anaduotai
: Atlantis Rises. Finch has MacGyver take a photo of him recovering the medal and then realizes the mount the coin in has a pressure switch. He substitutes a photo lens cap for the coin to maintain the pressure. Finch steps on a stone trigger just as MacGyver spots a spearhead in the opposite well. He pulls the professor clear just in time as the spear skewers the lens cap. However, a secondary trap goes off as the windows are sealed off and tons of gravel pours into the chamber. Finally there is only a little bit of air space at the top and Finch wonders how they're going to get out.
London, England: Five Years Later
Finch is giving a presentation to the Royal Academy of Archaeological Science on how the people of Atlantis built their city of art and science on a volcano. They worshipped a mysterious object called Torch of Truth, possessing light and wisdom. Finally the volcano erupted and the few survivors hid their treasure in a place called the Tower of Fear, and wrote their story in a book of platinum pages. In 950 B.C., a Greek scholar, Solon, discovered two relics of Atlantis in Egypt: the book and the Torch. He gathered his disciples and gave them an ark in which he locked the Torch of Truth. He then took the key and the book and went to search for Atlantis, and disappeared into history. Five years ago he found the key at Thera and proposes to follow Solon's footprints and find the treasure. The director informs him that they only fund serious expeditions and insist that the key will stay in the academy's collection. The director suggests tat the board reconsider Finch's tenure.
The Balkan Peninsula: Several Months Later
MacGyver and Atticus enter the catacombs beneath a military base during a civil war. Atticus explains that his disciples fled Athens and fled to England. They formed the Cult of Solon and their descendents lived peacefully for centuries until the Romans hunted them down. The few survivors fled England and came to the catacombs in the Balkans. Atticus assures MacGyver that the soldiers have no idea the catacombs are there.
Above ground, a soldier finds footprints leading into the catacombs and calls in Colonel Petrovic.
MacGyver and Atticus get to the oldest part of the catacombs and MacGyver finds a sigma, the sign of Solon, on a skull. He turns the skull and a panel opens to reveal the Ark of Solon. Atticus reads the inscriptions, which speaks of offering the Torch of Truth to the Temple of the Ages to reveal the treasure of Atlantis. MacGyver starts to remove the Ark but Petrovic and his men arrive to arrest them.
Petrovic takes them to his headquarters and tortures them, assuming that they're spies. MacGyver points out that the area is under a ceasefire by the UN. The colonel isn't impressed and insists on pursuing his agenda of ethnic cleaning. MacGyver leaps up to grab him and is quickly beaten down. Petrovic takes his Swiss Army knife and the Ark and leaves with his men after activating an electrified section of the floor in front of the door. Once he's gone, MacGyver reveals he grabbed Petrovic's cigarette lighter. He balances on his chair out across the electrified floor while Atticus explains that he deceived MacGyver and that his tenure was revoked. MacGyver uses the cigarette lighter to heat the lock and then swings a light bulb into the lock. The guard comes in and the two men feign unconsciousness. Once the guard comes in, MacGyver uses the chain to slam the door into him, knocking him out. MacGyver then uses the spring action from his rifle to get their manacles open. There's only one gate out. MacGyver ducks into a tent and finds local clothing for himself and Atticus.
As Petrovic leaves his office, the colonel is unaware that the Ark has magnetically pulled MacGyver's Swiss Army knife toward it. Atticus and MacGyver come to get the Ark and notice an old scratch. MacGyver picks up his knife and they realize the Ark is magnetic. They grab the Ark, hide it beneath a coat, and head for the gate. When soldiers arrive, they retreat to a garage and try to steal a jeep. They realize there's no engine and MacGyver bolts the door.
Petrovic realizes that the prisoners have escaped and sounds the alarm. Meanwhile, MacGyver attaches two missile propulsion systems to the rear end of the jeep. Petrovic notices the garage and orders his men to open it up. MacGyver finishes rigging up a grenade to the rest of the weapons in the garage. As the soldiers break open the door, MacGyver triggers the missiles and the jeep shoots toward the gate. The garage blows up behind them and MacGyver fires a mounted missile launcher to bring down the gate to make good their escape.
At the university, science professor Kelly Carson is giving a lecture to her class when MacGyver comes in. Once the class ends, MacGyver brings her an apple as a bribe to ask for her help. She notes that she didn't think he needed anyone's help. He shows her a sample off of the Ark and admits that Atticus obtained it. Kelly warns that her grandfather still isn't very fond of Atticus. She agrees to analyze the sample. Professor Simon Carson, her grandfather, arrives from Greece and apologizes for missing her lecture. He remembers Atticus and MacGyver almost getting killed at Thera and is unimpressed with Atticus' newest discovery. He promises to take a look at it later and goes to take a look at it before returning to Greece.
Once he leaves, Kelly admits that he came to England to talk her into accepting tenure. As Kelly runs the test, she admits that her grandfather prefers her to stay at university and have a safe career. MacGyver gets her to admit that she wants a challenge and see the world. He tells her to do it but Kelly admits she doesn't want to disappoint Simon, who raised her after her parents died. Kelly admits she had a crush on MacGyver but the analysis is completed before she can say more. Kelly determines the Ark was made in the sixth century B.C. but the tool that dented it was made by a tool of tin made near Exeter, Cornwall. Kelly asks to go with him to the academy to see Atticus.
As they walk to the academy, Kelly admits that her grandfather is unwilling to see the books on Atlantis changed. As they enter, a thief dressed as a janitor radios Lord Cleeve at his manor. He informs Cleeve that MacGyver and Kelly have arrived to open the Ark. Cleeve tells him what to do.
Carson insists that the medallion and the Ark are unconnected even though they have the same reference to Atlantis rising. The same riddle about using the Torch at the Temple to release the truth is on the Ark. There are symbols representing the various Greek gods, including Hecate, the demon of the night. Carson dismisses Atticus' theory and the director arrives to reveal that he talked to the Balkan authorities, who have claimed the Ark is a national treasure and they want it back. As the director removes the medallion, MacGyver notices that it's magnetized just like the Ark. Atticus attaches the medallion and open the Ark but there's nothing inside. He wants to take the Ark to Thera but Carson refuses to let his work in Greece disrupted. Kelly tells her grandfather that she is plans to help MacGyver and Atticus find Atlantis. Carson accuses them of poisoning her granddaughter's mind and stalks off to take a plane back to Thera. The director orders Atticus to clear out his office and leave the academy.
As they leave, MacGyver figures that the Torch was in the Ark at one time, but the Cult opened it and removed the Torch. Cleeve's man overhears their conversation and then shoots the director with a tranquilizer dart. He manages to set off the alarm as he collapses. MacGyver and Atticus go back to investigate and MacGyver tackles the man. He drops the medallion and knocks MacGyver into a display case, allowing him time to get away. Atticus secretly pockets the medallion while MacGyver follows the thief and leaps onto his fake cab as he escapes. The thief finally manages to shake MacGyver off, ditches the car, and heads for the docks. MacGyver can only watch as the man escapes via the Thames.
Inspector Rhodes investigates the theft and believes the thief plans to sell the item on the black market. He identifies the thief as Yannis Zavros, a former military officer who leads a cult of militant fanatics that believe they're the descendents of Alexander the Great and claim Macedonia as their birthright. They steal and sell artifacts to fund their cause and associate with Lord Cyril Cleeve. Atticus knows Cleeve as a former student interested in treasure who bought his title and an estate in Plymouth. Rhodes has no evidence against him and figures Cleeve has smuggled the medallion and the artifact out of the country.
Once Rhodes leaves, MacGyver demands to know what happened to the medallion. Atticus admits that he's holding it for safekeeping and takes them to his office. He shows them the medallion and figures that Cleeve stole the Ark to gain the instructions to find the treasure. Atticus explains that they have only two days to find the treasure, when the first line of Solon's riddle comes true. A reference to the gods marching in rank indicates a planetary and lunar alignment that happens only once every five hundred years, and the next alignment takes place in two days. The "Tower of Fear" refers to the Greek word for fear: Thera. Atticus finds a photo of himself and Carter from years ago, standing near the active volcano of Thera. The professor believes the cult hid the Torch of Truth in their caves at Exeter.
The trio goes to the cave and finds inscriptions representing Atlantis that the cult took from the platinum book. MacGyver notes that the cult thought that Solon was coming back so they hid it where only he could find it. He finds the Riddle of Solon written on the walls and an altar with a metallic hoop. MacGyver realizes the entire chamber is a giant Ark and the medallion is the key. He places the medallion in the center of the hoop and it hangs suspended in the magnetic fields. The hoop on the altar turns on its own and a rock wall slides aside to reveal a golden staff with an enormous crystal on the top: the Torch of Truth. MacGyver spots a stalactite mounted in the ceiling and removes the Torch, but nothing happens. Cleeve and Zavros arrive and Cleeve tells them to give the Torch to his partner: Atticus.
Cleeve ties up MacGyver and Kelly and leaves them in the Torch chamber. Atticus insists that their agreement was no killing, but once he leaves, Zavros seals the chamber. The stalactites start to shoot down from the ceiling and MacGyver uses one of them to cut their ropes and they get out just before the chamber seals for good. MacGyver admits he's disappointed at his old mentor betraying him. They realize that Cleeve will go to his estate with the Torch.
Kelly and MacGyver sneak onto the grounds and spot them preparing to leave by plane. MacGyver goes in on his own and gets to the study where Cleeve is boasting of his triumph. Atticus is shocked that Cleeve plans to buy his way into the history books.
Outside, Kelly goes to the plane and throws away the ignition key. She then uses the radio to call for help but Zavros soon captures her.
MacGyver listens as Atticus refuses to drink with Cleeve, admitting he was forced to help Cleeve. Zavros returns with Kelly and figures MacGyver is nearby. Kelly refuses to tell them where MacGyver is. MacGyver props a candle in the hands of a suit of armor and rigs a string from the hand holding the mace to a table of china. He lights the candle and then turns himself in before Zavros can start beating Kelly. MacGyver informs Atticus that his partner tried to kill them, and that he brought the police with them. The candle burns through the trigger rope, distracting Zavros long enough for MacGyver to disarm him. As they run out, Zavros tries to shoot them and Atticus kicks the gun out of his hand and assures MacGyver he's on his side.
Outside, MacGyver spots the plane and Kelly is forced to explain that she threw away the key. MacGyver uses his knife to flip the magneto switch and they fly away just ahead of Zavros and Cleeve opening fire. Atticus apologizes and admits that he thought he could control Cleeve. He was frightened and desperate once he lost his academy position. Atticus insists that the discovery of Atlantis could show that people lived in peace and harmony and still could. MacGyver warns that Cleeve and Zavros will come after them.
The trio flies to Greece and the Tower of Fear. The last time it erupted, it destroyed half the island. They land and take a jeep to the nearby archaeological site where Professor Carson works. Cleeve and Zavros have gotten there first and knocked out Carson, badly injuring him. They call in a doctor to tend to his concussion, and the man warns that he's too weak to be moved. Kelly tells MacGyver and Atticus that her father will be okay but Cleeve has taken the maps and charts of the volcano. They have less than 12 hours to find the temple. MacGyver notices that the lid of the Ark is not magnetic. He cuts open the inside of the lid with his knife and finds a secret compartment containing a platinum page from Solon's book. It's covered in unknown markings and holes. MacGyver has Kelly take them to the crater.
They arrive at the ruins of the temple, built over a series of sulfuric fumaroles. MacGyver finds a tunnel and they enter. Inside is a temple with a Copernican model of the solar system, built thousands of years before Copernicus. A vent in the roof reveals the planets coming toward alignment, causing the volcano to become unstable. They find a door with the mark of Hades and open it to find a series of gas jets and the burnt corpse of Zavros. MacGyver realizes the floor has a pressure trigger. Cleeve comes in and notes that Zavros tried to betray him and head for the treasure first.
Drawing a gun, Cleeve forces MacGyver to find a way to deactivate the fire trap. MacGyver studies the Copernican model and realizes that Solon's riddle about the gods marching in rank refers to the model as well. He finds slots in the model and realizes that the platinum page is the key. MacGyver inserts the slot which unlocks the model and turns the planets into alignment, deactivating the fire trap. Kelly notices that there's a red planet, possibly a star, within the model.
Cleeve forces MacGyver and the others to pass through the gate, through the fire trap, and into the chamber beyond. The cavern is a vast chamber with a flaming lake and a huge set of chamber doors at one end. Above is another vent showing the planets coming into alignment. They find what appears is the statue of a man but they realize that it's Solon himself, caught in a volcanic eruption and covered in hot ash. The statue is holding the platinum book and Cleeve takes it.
As the planets come into alignment, they realize that Hecate has to appear. The red star on the model represents a meteor, which appears in the sky. The extra gravitational force from the meteor opens the temple doors and reveals an altar with more labeled slots and three urns. MacGyver realizes that the pages from the book summon the power. He takes the book from Cleeve and removes the pages, inserting each one into its respective slot. MacGyver explains that the pages are punch cards and the altar is a computer running on geothermal power. He inserts the Torch, which acts as a lever to activate the mechanism and channel heat to drive the computer. A platform holding treasure chests rise up from the water.
Cleeve runs to open them and discovers they hold nothing but scrolls. He tears them apart looking for the treasure and MacGyver and Atticus explains that the scrolls contain the true treasure of Atlantis: knowledge. As Cleeve rips apart more of the scrolls, Atticus tries to stop him and is brushed aside. MacGyver tackles the treasure hunter and knocks him into the water. The volcano becomes active and they have no choice but to flee. However, the tunnel leading out collapses.
With time running out, MacGyver shuts down the steam engine and has Atticus block one of the pipes with his jacket. MacGyver then uses a funnel-like device, places it over the second vent, and attaches a rope. Finally, Kelly reactivates the steam engine and the funnel is expelled, shooting up out of the vent to hook up above. They reactivate the mechanism again after the loop of rope to the gears. The gears move the rope, carrying them up one at a time to the surface. MacGyver goes last but the gear jams leaving him stranded just short of the top. Atticus and Kelly pull on the rope and get him the rest of the way up. Kelly kisses him and they watch as the temple is consumed in flames.
Later, Atticus gives a presentation on the true history of Atlantis to a classroom of children while MacGyver, Kelly, and Simon look on.