Sora, Donald & Goof land in the New Groove World and crash into Kuzco's palace. Kuzco is upset and summons his guards. " Sorry, but you threw off the Emperor's groove !" they shout and tosses S D G into the dungeons.
S D G manage to escape the dungeons and they accidentally find Yzma's "rollercoaster ride " and end up with Yzma's hidden lair and Sora feeling hungry and thirsty drinks an Illama potion, transforming him into an Ilama.
Yzma and Kronk stroll in, so they have to hide and escape quickly. While trying to flee, Sora is split up with Donald and Goofy and is knocked out by Kronk with a frying pan Rapunzel-style. " Huh, two Kuzcos " ? Kronk says, as he skips away with a knocked out Sora and Kuzco in his bag.
Ilama! Sora wakes up in an Ilama farm with Pacha. Donald and Goofy reunite with him, as they try and support Sora from his new change. Cue Kuzco arguing with Kronk. Goofy says something like "Huh, he's been transformed into an Ilama too, maybe they can help us, Hyuck !"
Cue the middle part of the movie with Kuzco, Pacha, Sora, Donald and Goofy traveling back to the palace, with jokes, silliness, and jabs at the 4th wall.
Then, in the end, the game sets you up for an epic "heartless " battle, summoned by Yzma, but then the Heartless just transforms into an adorable kitten, that licks Sora's face. Donald kicks it away, and Kronk calls him a "bully". Kuzco and Pacha get the potion back, and Sora is back to his human self again.