Nate and Harry Flynn, an old acquaintance and partner in crime, break into the Istanbul Palace Museum in search of a clay oil lamp related to Marco Polo.
Polo's fleet left China with 600 passengers aboard fourteen ships loaded with treasure from the great Kublai Khan. It landed in Persia a year and a half later, diminished to one vessel and eighteen passengers. Polo documented every detail of the expedition - but did not disclose the fate of the missing ships and passengers.
The lamp reveals that Polo's fleet was caught up in a tsunami off the coast of Borneo and that the cargo was from Shambhala. Believing that the Cintamani Stone may still be there, Nate prepares to head out. Betrayed by Flynn and captured by the Turkish police, Nate spends the next three months in jail.
Bailed out by Sully and Chloe, an old flame, they head out to catch Flynn. Flynn and his client Lazarevic are close to finding the "Buddhist holy grail", a perfect raw sapphire worth hundreds of millions of dollars. Following the clues, Nate finds himself in the Tibetan mountains in a monastery where he finds the entrance to Shambhala. Surrounded by Lazarevic's men, they all enter the city and find it overgrown with the Tree of Life.
Entering, the men are attacked by the guardians of the city, allowing Nate to escape. Making his way through the city, Nate enters a pyramidal temple to find the Cintamani Stone. Realizing that the stone is in fact amber from the trees sap, not sapphire, it becomes clear that the Tree of Life is the real treasure.
At the base of the tree, Nate enters a showdown with Lazarevic. Imbued with the power of the tree's sap, Nate uses the sap's explosive reaction to damage Lazarevic and win. As the Tree of Life dies, Nate and the others escape.