In The Land of Spain in 1519, Sora and his friends met two wanted con artists, Tulio and Miguel, who win a map purportedly to the city of gold, El Dorado along with a large number of other valuables by cheating at a game of dice (though the map itself was won fairly). Chased by an angry bull and the city's guards, the two inadvertently and our heroes hide themselves on the ship belonging to Herman Cortés and his troops as they set off to the New World. The two along with our heroes are captured and sent to the Brig, but manage to escape to via rowboat, inadvertently bringing along Cortés' horse Altivo, and eventually end up ashore on the New World, where Miguel recognizes landmarks shown on the map. The 18 follow the map and end up where the map marks the entrance to El Dorado, but find only an enscribed monolith waiting for them. As they try to determine what to do next, a young tribal woman is chased by a group of guards, and Tulio, Miguel, and Sora and the others step in to protect her. The guards believe the two to be gods as shown on the monolith, and escort them along with the woman along a river cavern to El Dorado, truly a city made out of gold.
Tulio and Miguel are introduced to the city's elders, Chief Tannabok and high priest Tzekel-Kan (whom Hans, Pete and Barnaby works for). After appearing to stop the eruption of a nearby volcano by their words only, Tulio and Miguel are proclaimed to be gods despite Tzekel-Kan's suspicions, and are treated luxuriously. The woman they rescued from the guards, Chel, rapidly becomes aware of Tulio and Miguel's charade. She offers her silence and assistance and, in exchange, she is not punished for attempting to steal gold from the city and offered a trip back to "wherever you come from". After the night of a feast prepared by Chief Tannabok to honor them, Miguel and Tulio are shocked to find that Tzekel-Kan is ready to offer a human sacrifice, and insist that it be stopped, stating they will take the gold instead as their tribute. The two quickly conceive of a plan, and convince Chief Tannabok to build them a boat over the next few days so that the "gods" may return along with their tribute. While Tulio plans to wait out those days in their provided villa, Chel urges Miguel to go explore the city, allowing her to get romantically closer to Tulio.
Tzekel-Kan, finding Miguel playing ball with children in the streets, organizes a Mesoamerican ballgame match between them and the city's best players in the hopes that they will prove skilled enough to provide a modest challenge to the two. Miguel and Tulio quickly find themselves outmatched until Chel replaces the ball with a rolled-up armadillo that allows them to cheat and win the game. However, Tzekel-Kan catches a small cut on Miguel's forehead and is finally convinced that they are not gods, as gods don't bleed. Chel and Tulio are found kissing by Miguel, and thinking that Chel means more to Tulio than their friendship, Miguel falls out with Tulio. Later Tzekel-Kan, Pete, Hans and Barnaby brings to life a giant stone jaguar statue and unleashing an army of heartless and chases Sora and The Gang, Miguel and Tulio around the city, eventually leading them to the edge of a cliff overlooking a giant whirlpool. Tulio and Miguel use their con tactics to fake an argument and, in the resulting chaos, both Tzekel-Kan and the jaguar statue fall into the whirlpool. At the same time, Sora and the others placed the Hans, Pete and Barnaby send them into a another planet far away from El Dorado. When Tzekel-Kan emerges from the whirlpool, He finds himself far outside El Dorado at the feet of Cortés and his men. Cortés threatens him and asks where he got his gold earrings. Tzekel-Kan notices the way that Cortés and his man stand are similar to the stances of the real Gods in the monolith; believing that they are the true Gods, he begins to lead them to El Dorado.
Though Sora, the others, Tulio and Miguel are safe, the two wish to go separate ways: Tulio desires to leave the city with Chel and the gold and Sora and the others, while Miguel opts to stay along with Altivo. Though they each are certain of what they want, they are reluctant to part ways. With the boat completed, Tulio and Chel prepare to depart as they say their tearful goodbyes to Miguel and the people of the city. Then, Altivo spots smoke on the horizon, and a messenger informs Chief Tannabok that Cortés is approaching the city, led by Tzekel-Kan. Though Tannabok is ready to fight, Miguel warns him that the people of El Dorado could not defend against Cortés's forces. Tulio comes up with a plan to topple the statue at the river's mouth in order to create enough wave force to propel the boat and collapse the pillars supporting the cavern entrance, as to seal the entrance to El Dorado forever and keep its population safe. As Tulio and Chel depart, their sails catch and fail to catch enough wind to allow the boat to clear the falling statue; Miguel forgoes his chance to stay in the city and jumps onto the boat with Altivo's help to pull the sails free, allowing the boat to clear the statue. Tulio's plan works as expected, though the boat and all their gold is lost as it collapses the pillars. Cortés, his army, and Tzekel-Kan arrive to find passage sealed. Believing that there is in fact no El Dorado, Cortés and his men seize Tzekel-Kan and depart. Tulio, Miguel, and Chel reunite, and while disappointed about losing the gold, are happy to be alive and friends again, and they set off on Altivo, who still happens to be clad in golden horseshoes, towards their next adventure. Sora and his friends rode off into the sunset to seek their next adventure.
- Ratchet, Clank, Sly Cooper, Bentley, Murray, Spongebob Squarepants, Patrick Star, Mr. Krabs, Squidward Tentacles, Courage, Finn The Human, Jake The Dog, Leonardo, Donatello, Raphael and Michelangelo guest star in this film.
- Pete, Prince Hans and Mr. Barnaby will be working with Tzekal-Kan.
- The Heartless makes a cameo in this movie.
- Both Pete and Herman Cortés were voiced by Jim Cummings.