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.

After failing his "squirrel speak" quiz, Kuzco is forced to get tutored by Bucky the Squirrel, whom he really dislikes.

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.

Malina is supposed to be Kuzco's date for the Kuzcoteque, but he can't get past a tiny zit on her nose. When he tries to use one of Yzma’s potions to get rid of the zit, it ends up giving her the beak of a bird!

Yzma’s science class is dissecting frogs, so she turns Kuzco into one so he can be dissected! Instead, he becomes a “hero” known as the Red-Eyed Tree Frog Man.

Kuzco is having trouble with his knot tieing homework. He decides to steal Chaca’s. Meanwhile, Yzma turns Kronk into a Llama, who takes the homework and runs off.

Kuzco, Kronk and Malina are given a class assignment that involves their survival skills. They are forced to stay overnight in the wilderness without anyone or anything. Just when they finally get there camp set up, Kuzco accidentally gets it destroyed.

Kuzco struggles with a school fundraiser of having to wash carts for 100 KuzCoins. Then, Yzma turns him into an Elephant making matters worse!

Kuzco resorts to cheating and stealing Yzma's "inventions" during a required invention fair. He steals her Woodbot and it begins rampaging around the kingdom and it heads towards the school!

Everybody at school gets their grades. At lunch, Kuzco, Kronk, and Malina share there grades. Malina finds out that she got an A – and freaks out. Then, because of that she gets kicked off of the cheerleading squad. Malina starts to have an identity crisis and decides to act like school baddie Roxy. Then, Kuzco and Kronk drink a magic potion that turns them into girls in order to get their friend back.

Pacha and Chicha decide to go to a spa for their wedding anniversary. Since no one else is able to babysit they ask Kuzco. Kuzco agrees, but only because he wants alone time with Malina. Then, while Kuzco thinks they are sleeping they disappear! They have gone off to find the spa and give their parents their gift. Kuzco and Malina search for them, but the kids end up in Yzma’s lab!

Kuzco teases a student named Kavo thinking he is just joking around. Kavo, who gets mad about it, decides to beat Kuzco up. Kuzco then hides all over the school and even turns himself into a cat to avoid Kavo.

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.

When Kuzco gets bored with school paper that Malina helps to make, he replaces her and makes his own all about him and untrue stories, thus turning it into a tabloid.

In Home Economics class, everyone is given a kitten to take care of for a week. Once again, Yzma tries to make him fail by turning the kitten into a jaguar.

When Kuzco creates Kuzco Allegiance Day, Mr. Moleguaco assigns a class project where one student is emperor for a day. So Malina is chosen to randomly draw who will the emperor. When Kronk is chosen as the emperor for a day, it teaches Kuzco that being a peasant is harder than it looks. But when Yzma finds out that Kronk is emperor, he has Kronk tell Kuzco and the rest of the students that they have to bow down to him. However, Kronk fires Yzma. So she helps Kuzco and Malina wear down Kronk with the one thing an emperor hates the most.

After being introduced to fortune cookies, Kuzco starts to believe them and begins to follow everything they say. Yzma tries to trick Kuzco into turning over the kingdom to her by placing fake fortunes into fortune cookies; one of which that states that if he doesn't turn over the kingdom by 5:00 PM he will turn into a hairless sloth.

When Kuzco's attempts to earn money for the cartcycle that he wants to buy fail miserably, he turns to an old legend about magical creatures that are supposed to hand over their gold to you if you catch them.

Kuzco and his class visit the ruins of Micchu Pachu, which is actually an amusement park. Kuzco is scared but doesn't show, he wants to go home but if he does he will fail. However, an anteater skeleton appears and goes after everyone.

After a mask is stolen, Yzma wants to blame Kuzco for taking it. Kuzco, Malina, Kronk, Yzma, and the Security Camera all tell their side of the story. That is, until Pacha tells them the truth.

For Kuzclub Week, everybody has to join a club for a week or will fail. Kuzco joins the Jr. Chipmunks hoping for an easy time. Yzma's nephews, Zim and Zam, try to make sure Kuzco doesn't get a badge so he can't pass.

The annual "Clash Of The Families" is set to start and Kuzco decides to compete with Pacha's family. so he can dance with Malina at the dance at the end. However, when Pacha and his family go canoeing, there is no room for Kuzco which makes him feel like is is not wanted.

A new kid arrives at the academy. His name is Oscar and claims that he is an emperor. He adores Kuzco which makes Kuzco believe that he is Amzy in disguise, so he goes and tries to prove it.

Yzma finds out that when a student gets in trouble they get a ticket. If they have three then they are expelled. Knowing that Kuzco breaks a lot of rules, she makes Kronk an officer in order to expel Kuzco. However tables take a turn when Kronk breaks three rules and must know do what Kuzco wants or get expelled.

After getting fired for obvious reasons, Kronk moves in with Kuzco and Pacha. The entire family then warms themselves up to Kronk, much to Kuzco's jealous chagrin.