Uxie is mentioned once the player, their partner, and Bidoof reach base camp. A legend about Fogbound Lake and Uxie's ability to erase memories is told, leading the player to believe that Uxie was the cause for their amnesia.
When both the hero and their partner reach Fogbound Lake, they encounter a Groudon who guards the area. Upon its defeat, they find out that it was an illusion created by Uxie. Upon asking a question, Uxie confirms that he had no involvement with the amnesia, and never even came close to the two of them. He then shows the two, along with the guild members, a geyser filled with Volbeat and Illumise. He lets them go, warning them to keep this place a secret. However, some time later, Grovyle takes down Uxie and steals the Time Gear.
Uxie is mentioned when the player faces off with Mesprit at the end of Quicksand Cave, who says that the two had spoken through telepathy. Later, with this hint, Dusknoir is able to infer that Grovyle had not yet stolen the last of the Time Gears, guarded by Azelf.
After Azelf successfully defends his Time Gear from Grovyle, Uxie, Mesprit, and Azelf join forces with Dusknoir to set a trap for Grovyle. After Grovyle is captured, Uxie, as well as Mesprit and Azelf, makes a promise that all the Time Gears will be restored to their rightful places.
After the player defeats Primal Dialga, the player's team is allowed to try to defeat a level 42 Uxie in the Fogbound Lake, where if they win, Uxie will join the player's team.