Long ago, somewhere deep in the jungle...
Kuzco is a bratty, arrogant Incan emperor who uses his position of power to mistreat his subjects while he lives it up in luxury. He summons Pacha, the leader of a local village, and announces that he plans to destroy his village to build his giant summer home "Kuzcotopia", as part of his eighteenth birthday celebration, despite the latter's objections. Meanwhile, Kuzco's former advisor, Yzma, is angry following his dismissal of her and plots to poison him so she can take over the throne. However, the plan goes awry when she and her moronic assistant Kronk mix up the potions and Kuzco ends up transforming into a llama.
After knocking llama Kuzco out, Yzma orders Kronk to dispose of him; but a stroke of conscience prevents him from doing so, and he loses him on a cart, which turns out to belong to Pacha. After arriving at Pacha's home, Kuzco comes to and orders him to take him back to the palace; when Pacha refuses unless Kuzco builds his summer home elsewhere, the young emperor wanders off into the jungle and gets attacked by jaguars. Pacha rescues him and Kuzco begrudgingly accepts his deal to escort him home, and the two eventually learn to co-operate. Meanwhile, Yzma takes over and when she finds out Kronk did not kill Kuzco, the two villains set out to find him. Both parties arrive at a diner, completely unaware of the other's presence. When Pacha eavesdrops on Yzma's plans, Kronk almost recognizes him. When Pacha tries to warn Kuzco that Yzma is planning to kill him, the latter refuses to believe it, and Pacha leaves, but then overhears Yzma's plans himself.
Realising that nobody in the kingdom misses him due to his selfish personality, Kuzco resigns himself to life as a llama, before running into Pacha, and the two reconcile. Meanwhile, Kronk finally realizes how Pacha and Kuzco are connected, and he and Yzma arrive at his house, pretending to be distant family members. Pacha has his family stall Yzma, giving him and Kuzco a head start back to the palace. The two arrive at Yzma's lab to retrieve potions, but discover that she has beaten them there. Yzma orders Kronk to kill Kuzco, but he can't bring himself to do so, so Yzma gets rid of him. While running from the guards, Kuzco tries several potions until only two are left. Yzma accidentally lands on one of them and is transformed into a kitten. She, Kuzco and Pacha fight for the final vial, but Yzma is unexpectedly foiled by Kronk. Kuzco drinks the potion and is turned back into a human.
Now having gone through a change of heart, Kuzco makes amends with those he has offended and builds a scaled down summer home on an empty hill near Pacha's village, and invites Pacha's family to join him. Meanwhile, Kronk becomes a scout leader and trains new recruits, including Cat Yzma, to speak squirrel.
