Two years after the events of the first game, treasure hunter Nathan Drake (Nolan North) is approached by former associate Harry Flynn (Steve Valentine) and Flynn's girlfriend Chloe Frazer (Claudia Black) to help steal a Mongolian oil lamp connected to Marco Polo's doomed 1292 voyage from China. The group plans to cheat Flynn's client and take Polo's treasure for themselves. Unbeknownst to Flynn, Chloe and Nate had worked together before, and Chloe plans on blackmailing Flynn and escaping with Nate and whatever treasure they find.

Nate and Flynn break into a museum in Istanbul and find the lamp, which contains a map and flammable resin that reveals Polo's fleet was shipwrecked in Borneo, and was carrying the Cintamani Stone from the fabled city of Shambhala. Flynn double-crosses Nate, leaving him to be arrested.

Three months later, Chloe helps free Nate with his longtime friend Victor Sullivan (Richard McGonagle). She reveals that Flynn is working for Zoran Lazarević (Graham McTavish), a Serbian war criminal seeking the stone. In Borneo, Nate and Sully infiltrate Lazarević's camp, with Chloe as a mole. Nate discovers that the stone never left Shambhala, and locates a temple containing the bodies of Polo's crew, as well as a phurba and map detailing that its carrier will gain passage to Shambhala through a temple in Nepal. Nate and Sully escape after being cornered by Flynn and his men.