Kuzco faces his first threat of losing his position as Emperor when he struggles in P.E. and his teacher threatens to flunk him if he can't win a race with Kronk. However, Principal Amzy (who is really Yzma) tells Kronk to turn Kuzco into a turtle so he has no chance of beating Kronk, but instead, Kronk gives Kuzco the wrong potion and he ends up as a rabbit.

Kuzco wants to buy a new bike that is really expensive, but he finds out that he can't dip into the Royal Funds unless he's sick, so he decides to fake sick by coloring orange spots on his face with Chaca's orange crayon.

Everyone is told to write a paper on their best friends. Kuzco, who doesn’t have any real friends, makes his person up. Then, we he is told to bring this person in, someone exactly like him does show up! What Kuzco doesn’t’ know, is that it is a clone made by Yzma.

Yzma tries to trick Kuzco into thinking he saw a U.F.O.

Kuzco thinks that Llama herding looks easy, so Pacha makes him do it for a day. However, the Llamas end up drinking some of Yzma's potions and are turned into demons. Meanwhile, Kronk, who also had some of the potion, is trying to get a meal at Mudka's, but everyone keeps banning him.

When Yzma gives Kronk the assignment of disintegrating Kuzco, Kronk consults his shoulder angel and devil. However, the two of them get into another fight and Kronk tells them to go away. With those two gone, Kronk can no longer make decisions. Yzma then captures his shoulder angel in a cage, and gives the shoulder devil back to Kronk. This causes Kronk to agree with everything the devil says, which causes him to try and disintegrate Kuzco.

While lost in a storm, Kuzco, Kronk, Malina, and Guaca end up lost in the woods and wind up at Mudka's #13, a supposed cursed restaurant. They decide to stay there until the rain stops, against Kuzco's will. However, soon the secret of the restaurant is revealed when Kuzco wanders into unknown parts of the building.

It is time for the annual Cornivale celebration and Kuzco wants to avoid it. He fakes being sick and then decides to head to the beach for the weekend. However, his cab driver annoys him constantly and ends up getting them stranded in the forest and robbed. However, talking with the cab driver might be just what he needs to realize what is really important. Meanwhile, Yzma disguises herself and joins Pacha's family for Cornivale so that she can turn Kuzco into an ear of corn so that Pacha will eat him.

As Kuzco prepares to graduate, he must watch a Emperor orientation video. The video makes him question whether or not he can lead his people and if he really wants to become the Emperor again. Yzma, needing to make a last-ditch effort to prevent his graduation, decides to prey upon Kuzco's new insecurity. She gives him a potion that will turn him into a chicken forever. He decides to take it, and runs away and accidentally winds up in a Mudka's meat mug manufacturing plant. With Yzma becoming Empress inevitable, Kronk and Malina must find Kuzco and turn him back into a human so he can become Emperor.