The film opens with narration from Kuzco the Emperor of a vast land, in the form of a llama, telling the story of how his life as a ruler used to be and was ruined "for no reason". However, in his flashback he is shown to have been a rude, selfish king. After he fires his advisor, Yzma, for abusing her power, she and her henchman Kronk plot to usurp the throne. Meanwhile, Kuzco meets with Pacha, a kindly peasant of a man and tells him that he wants to demolish his family home to build himself a lavish summer home called "Kuzcotopia". Pacha protests, but is dismissed.
Yzma and Kronk later attempt to poison Kuzco, but end up giving him the wrong potion and accidentally turn him into a llama. Yzma orders Kronk to dispose Kuzco's body, but Kronk has a stroke of conscience and saves him, before accidentally losing him the back of Pacha's cart. Pacha returns home but does not tell his pregnant wife or children about Kuzco's decision. After awakening in the cart, Kuzco reveals himself as a llama and orders Pacha to take him back to the palace, but Pacha will only do so if Kuzco agrees to spare his family's home. Kuzco haughtily sets off into the jungle alone, before being ambushed by jaguars and Pacha rescues him. Kuzco and Pacha then make a deal about going to the palace.
Meanwhile, Yzma takes the throne, but Kronk then reveals that he lost Kuzco. The two set off to find him and finish the job. Pacha and Kuzco are almost back to the palace when Pacha falls through a bridge and Kuzco refuses to help him up, admitting he never meant to keep his promise. However, he soon finds himself in danger too, and they work together to save both their lives. Without the bridge their journey is delayed, giving Pacha hope that Kuzco will change his mind. Kronk and Yzma stop at a jungle restaurant at the same time Kuzco and Pacha are there disguised as a married couple. Neither party realizes the other is there until Pacha overhears Yzma and Kronk talking about trying to kill Kuzco. He tries to warn Kuzco, but Kuzco does not believe him and the two separate angrily. Kuzco then overhears Yzma's plot to kill him, but when he tries to return to Pacha, he finds that he has already left and is unable to find him.
The film then returns to the opening scene, with Kuzco lost in the jungle alone. However, he is soon reunited with Pacha, and they enlist the help of Pacha's family to keep Yzma and Kronk occupied while they escape. The race to the palace seems to end with Yzma and Kronk falling off a cliff, but they still inexplicably reach the palace first. Yzma orders Kronk to kill Pacha and Kuzco, but Kronk gets into a conversation with his shoulder angel and devil, and finds he cannot bring himself to commit murder, which leads Yzma to insult Kronk and his cooking and resign to do it herself. Yzma calls the guards who do not recognize Kuzco and attack the two of them, while Pacha and Kuzco take all the potions they can carry in hopes that one will turn Kuzco back.
After several guards are transformed into animals while testing potions and Yzma is transformed into a kitten, Pacha and Kuzco work together to try and get the last vial. Yzma snatches it at the last moment, but is unintentionally foiled by Kronk. Now a human again, and a more selfless ruler, Kuzco decides to build his summer home elsewhere, and Pacha suggests a neighboring hilltop. In the end, Kuzco is shown living next door to Pacha's family in a modest cabin, sharing a swimming pool with Pacha and his family. Yzma, still a kitten, grudgingly joins Kronk's Junior Chipmunk troop, along with Pacha's children.
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