The narrative opens with a quote attributed to Marco Polo, "I did not tell half of what I saw, for I knew I would not be believed." The plot revolves around the doomed voyage home of Marco Polo from China in 1292. After spending almost 20 years in the court of the Mongol Emperor Kublai Khan, Marco Polo departed with fourteen ships and over six hundred passengers – but when he arrived in Persia a year and a half later, only one ship and eighteen passengers remained. Polo never revealed what had happened to the lost ships.
The story begins in medias res, with a wounded Nathan "Nate" Drake (Nolan North) waking up to find himself in a train hanging off a cliff with a bloody stomach wound. Through flashbacks, it is revealed that former associate Harry Flynn (Steve Valentine) and old girlfriend Chloe Frazer (Claudia Black) approached him with a job to steal a Mongolian oil lamp from an Istanbul museum. Nate accepts the job when he learns that the lamp may lead to the treasure of Marco Polo's lost fleet. Flynn and Drake acquire the lamp, which contains a map showing that the lost fleet had been transporting the Cintamani Stone from the mythical city of Shambhala (better known as Shangri-La) before being thrown ashore in Borneo by a tsunami. Taking the map, Flynn double-crosses Drake, who is arrested and imprisoned. After three months he is released with the help of old friend Victor "Sully" Sullivan (Richard McGonagle) and Chloe. Chloe, who claims to have had no knowledge of Flynn's treachery, had asked for the help of Drake's friend to secure his release.
Nate and Sully follow Flynn and his boss Zoran Lazarevic (
Graham McTavish), a
Serbian war criminal who is widely thought to be dead, to Borneo. With the help of Chloe working within Lazarevic's camp as a mole, they discover that the lost fleet never actually possessed the Cintamani Stone. They locate a tomb containing the bodies of Polo's passengers, as well as a
Tibetan phurba and a letter from Polo saying that the next clue is in
Kathmandu,
Nepal in a temple. Flynn and his men appear in the tomb soon after and take the letter, while Nate and Sully escape by jumping off a cliff into a river.
While Sully backs out, deciding that the quest is too risky for him, Nate and Chloe head to Nepal, finding conflict as Lazarevic's mercenary army ravages the city looking for the right temple. After surmising that the temple they are looking for is adorned with one of the symbols on the phurba, the couple survey the area from the rooftop of a local hotel, finding its location.
En route to the temple, the pair runs into Elena Fisher (Emily Rose) and her cameraman Jeff (Gregory Myhre), who are tracking down Lazarevic to prove he is still alive. The four reach the temple, but Elena is still worried about that something is amiss, Lazarevic not needing the money. Nate and Chloe leave them anyway and discover that the stone and Shambhala are in the Himalayas. As they are about to leave, they are ambushed and Nate runs out to help Elena and Jeff (who were left at the temple entrance) to discover that Jeff has been shot by one of Lazarevic's men. Despite Chloe's insistence to leave Jeff behind, Elena and Nate insist on helping him and they push on until they are caught by Flynn and Lazarevic. Chloe reluctantly pulls her gun on Nate to protect her "cover", while Flynn has his men take Chloe to the trian yard, Lazarevic kills Jeff. Lazarevic takes the map from Drake and leaves Flynn to kill him and Elena. However, Elena punches Flynn when he tries to get her up and Drake punches his guard and they manage to escape.
