Background

Nate and Elena fighting off Pirates

Nate and Sully discussing El Dorado

The game picks with Nate and Sully who are exploring a jungle. They are following the map in Drake's diary to this location and are looking for El Dorado. They arrive at the location but don't see anything. On further investigation, they find an area in the forest that had a wooden floor instead of the regular soil. They break the floor and unearth a secret passage to an underground facility. Following instructions in Drake's diary they are able to make it to a chamber which looks like it has been stripped clean. Nathan finds a helmet on the floor that he examines and concludes that the Spanish had already gotten here and cleaned the place out. Sully becomes frustrated and reveals to Nate that he is in a lot of debt due to some bad deals he had made and he needs this to be more than just another wild goose chase. They move forward and after a nerve racking run across a crumbling wooden bridge they make it to another chamber. They find a recess on the wall and on examining it Nate believes that there must have been a large gold statue placed here and was the center piece around which the facility was built. They look at paintings around the recess and see people worshipping the statue and Nate realizes that that there was not a city of gold but rather it was a golden statue and that El Dorado actually meant "the golden man". They see grooves on the floor that indicate something was used to move the statue and they follow it to the back of the chamber, whose wall had been blown out to make a shortcut to remove the statue.

U-boat stuck Up-River

After escaping on Elena's jeep, they take Sully's airplane to the Island whose co-ordinates they had found on the map. Elena had agreed to help Nate in exchange for the story about the treasure and Nate needed all the help he could get. While they are making their way to the island their plane is shot down and they are forced to parachute off. Elena takes off first while Nate does so later and both of them end up in different parts of the Island when they land. Nate had forgotten to pick up the map when he had parachuted of the plan so first he decided to get to the remains of the plane to see if the map was still there.  He reaches the area where the plane crashed to find that the ship was stuck on a tree and using a rope he is able to get up to the plane. He finds the map still on the dashboard of the cockpit and just as he about to leave he sees Elena's parachute stuck on a tower in a distance. Nate makes his way towards the Fortress on whose tower Elena's parachute was. As he gets there he sees here off in the distance and again makes his way towards her and finally catches up to her as she filming the island oblivious of what happening around her. Before he could get her attention he realizes that  there are two pirates you just saw her and ere about  to shoot at her. Instinctually, Nate fires open the pirate who turns around and hits an area near him with a grenade launcher knocking him out cold.

Eddy Raja with his Golden gun

Nate and Elena escaping from Eddy's goons

Trivia

1. As fans of the independent cult television series Firefly, the Naughty Dog crew has admitted partially basing the image of main protagonist Nathan Drake on Firefly's protagonist, Captain Mal Reynolds, played by Nathan Fillion.
2. Further tying into Uncharted's relevance to Firefly, the game's score was composed by Greg Edmonson who also composed the soundtrack for Firefly.
3. When played on a Japanese PS3 (regardless of which region coded game one plays) blood does not appear when shooting enemies. Similarly, this method of censorship was also used for the earlier PS3 exclusive game Resistance: Fall of Man. 
4. The foreign language used prominently at certain points during the game is Indonesian, spoken by both protagonists and antagonists alike.
5. There are references to past Naughty Dog games strewn throughout Uncharted; for instance, a Precursor Orb from the Jak and Daxter franchise can be found as a hidden treasure.
6. In a few select areas within the United States, Uncharted was released on November 16th, 3 days prior to it's official scheduled release, November 19th.
7. The name of the plane was Hog Wild, this is the name of a level from the original Crash Bandicoot game that was also made by Naughty Dog