Kuzco and Malina head to Mudka's to eat. When Malina is displeased with Yata and the overall service, she gets a job and starts to improve their service. However, when her service makes Yata look bad, Mudka Junior, the owner, fires Yata. Now Malina, Kuzco, and Yata have to think of a way to get Yata's job back.

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.

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.

Kuzco invites Malina, Kronk, Yata, and Guaca over to play games, where they discover Guaca's \"fear\" of drawing. His father wants him to be an artist, so he entered him in the art competition to be held the next day. Kuzco hates seeing Guaca so depressed (since he keeps spilling his drinks), so he sneaks into Yzma's lab to find a painting potion. When it turns out that Yzma used the last one, Kuzco must make another one. When he goes to test it at the art fair, his pterodactyl drawing comes to life and takes Guaca's father for a ride! Now it is up to Guaca to save his dad.

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.

When Kuzco's class visits the museum, an ancient tablet reveals that Kuzco is not the true heir to the throne, Guaca is! Guaca immediately takes over the palace and starts to treat even Kuzco unfairly. Yzma decides to take advantage of this and trick him into hiring her as his adviser, however none of her old tricks work on Guaca due to his obsession with Kuzco. Then he demands that Malina become his empress or he will build a store over her house. Kuzco and Malina then decide to seek out a special chalice that will reveal the true heir to the throne.

Kuzco's class is assigned to research their family tree. When Kronk asks his father, he discovers that he is actually from Kronkenitza, which causes Kuzco and some other kids at school to make fun of him for being different. Even Yzma wants in on the fun, so Kronk decides to leave and go to Kronkenitza. However, his leaving may not be a good idea, as soon his friends begin to miss him when some terrible things begin to happen. Meanwhile, Yzma's latest destroy Kuzco scheme involves cloning herself to win a contest.

When a new card game becomes the latest craze, Kuzco rushes to get his own set of cards. He then tries to rip off Kronk to get a powerful card, but it turns out that it was he who was ripped off. Now Kuzco will do anything to get the card back. Yzma decides to try and use the card to trade the rights to the throne. Meanwhile, Malina and Yata, who believe they are being mature by not being caught up in the latest fads, start buying all the coolest accessories.

Kuzco misses all of the room at the palace and is sick of sharing a room with Chaca and Tipo, so he puts them up for sale outside. Kronk comes by and offers to clean the house for them. However, this is a plan by Yzma. She wants Kronk to to find Kuzco's Emperor permit so that she can change it to make her Empress.

In her latest attempt to take over the empire, Yzma decides to make herself the new face of the ancient Halloween...with spooky results.

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.

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!

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.

Yzma's latest scheme to get rid of Kuzco is a little more simplistic then usual. She decides to just put him in a box and ship him away. When Kronk sets a trap for Kuzco, he also ends up capturing Malina, and shipping them to a deserted island. While Yzma decides to begin her palace remodeling, Kronk heads to the island to save Malina, and maybe Kuzco. In order to stop Kronk from rescuing Kuzco, Yzma heads to the island. Meanwhile, Malina ends up becoming an idol for the monkeys, who do anything she wants. Kuzco then gets them to worship him, but the two end up being sacrifices to their real idol, a giant monkey.

It is time for the annual Nut Festival and Kuzco wants no part of it, so he heads to the river. When Bucky bothers him, he throws a nut which ends up breaking a dam and washing away the festival. He blames it on the squirrels, so the villagers decide to gather up all the squirrels and ship them out of town. Yzma takes advantage of this and uses a pie to turn Kuzco (and accidentally Kronk) into a squirrel.

A guy from Kuzco's past comes to get revenge on Kuzco for falsely imprisoning him for breaking Kuzco's statue seven years ago.

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 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.

Following Yzma's latest fail to destroy Kuzco scheme, Kronk convinces Kuzco to finally stand up to Yzma and get rid of her. Kuzco and Guaca team up to remove everything from her lab, which results in a potion battle between Kuzco and Yzma. Meanwhile, Yzma has promised to take Kronk to Pajama Llama on Ice if he tells her who gave Kuzco the idea to destroy her, which results in Kronk trying to figure out what to do.

Yzma hires an evil consultant, who ends up kicking her out of her own offices. Meanwhile, Kuzco starts to go "bad" and not listen to anyone.

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!

When Kuzco refuses to leave the mall, he gets into a chase with Officer Achamare and gets him fired. Since the mall needs security Kuzco is forced to do it. When the mall gets out of control, Kuzco tries to get Officer Achamare his job back. Meanwhile, Yzma and Kronk plan to break into Kuzco's money vault.

A charity bachelor auction is being held to raise money for charity, and Kuzco, Kronk, and Guaca will all be in it. When Kuzco insults Malina, she bids for Kronk instead to make him jealous. Kuzco then convinces Yata to bid for him to make Malina jealous. Then the four just happen to end up at the same restaurant for their dates, which turns the jealousy fest into an all out battle.

Yzma leaves for a week to pursue her dream of stardom. Since she can not trust Kronk to keep track of things, she leaves a robot version of herself to take care of things. When Kuzco turns his homework in late, he finds out that he can get Mr. Moleguaco to look at it if the principal tells him to, so he tries to get Yzbot from Kronk.

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.

Malina signs up for the "Save A Manatee Program" and is forced to take care of a manatee at her house. When the manatee, named Doyle, expects her to do all the work and messes up her room along with Kuzco, Malina tries to get rid of Doyle.

It is school picture day and Malina is making a big fuss about how her school picture must be perfect. When her picture ends up being bad, she rounds up all the yearbooks and destroys them. However, she forgets that a yearbook is locked in a Time Capsule in the temple. Now, her, Kuzco, and Kronk must get the yearbook before the temple is locked for 1,000 years.

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.

With the Kuz-Carnival coming up, Kuzco wants to go with Malina so they can go in the tunnel of love. However, she once again turns him down. This time it is because Ramon asked her to go. Kuzco decides to ruin the date., so he shoves Bucky in their popcorn, sprays Ramon with water, and even puts him into a arena with a hungry bear. But will his tricks work?

Yzma's latest scheme to rule the empire includes turning Kuzco into a puma. She plans to slip the puma potion into Kuzco's Meat Mug since that is the only thing he will eat. However, Kronk refuses to tamper with the recipe, so Yzma breaks into Mudka's and steals the recipe. When Kronk finds out, he and Kuzco head for Major Mudka's hut to get back the secret recipe. At the same time, Kronk and Yata try to get Kuzco to eat healthier.

Yzma comes up with the ultimate way to prevent Kuzco from graduating! She wastes school funds and the academy goes bankrupted, and Yzma tries to tear it town. Malina convinces Yzma to give them two days to raise enough money to save the school and she decides to do a musical. The plan seems to be ruined prematurely when no one is good enough to be in it. However, things are saved when Yata manages to get pop superstar Dirk Brock to perform in the musical. Now that Kuzco can't star in the musical, he tries to get rid of Brock (as does Yzma), but his advances could push Malina away from him.

Yzma's latest scheme to destroy Kuzco backfires and gives Kuzco superpowers, such as flying and x-ray vision. Kuzco then begins to treat his friends badly. Then, Yzma decides to take matters into her own hands, and gets superpowers of her own, and vows to use them to destroy Kuzco.

Malina is stressed out by the preparation for an interview for an internship at the teen magazine Incan Teen. She asks Kronk and Kuzco for help and they decide to teach her how to relax properly.

Kronk and Kuzco team up together for their school assignment and open a spinach puff stand. Although Kronk's puffs are a great success Kuzco takes over the team and turns the puff stand into a industrialized restaurant. Finally Kronk quits due to Kuzco's treatment opening his stand again while Kuzco ruins his restaurant.

When Kuzco is attacked by pumas, Pacha saves him, and Kuzco thinks it is because of his amazing dodging skills. When he brags about it at school, Guaca arranges a puma wrestling match for him, but will he be revealed a phony?

Yzma's plan to wipe Kuzco out of the Royal Records backfires when Kronk replaces Kuzco on the records after rescuing the Royal Record Keeper. To repeal this change Kuzco and Yzma team up until the former Emperor-to-be recognizes his chance and turns against her.

Malina and Kuzco attend Kamp Kuzco as tutors for a group of Junior Chipmunks. Soon Kuzco's statements about 'male advantage' lead the tutors to set up a race between the girls and the boys of the group. Through an attempt to ensure the victory of his boys, Kuzco gets himself and the girls lost in the jungle. So now Malina and Kronk have to rescue them and even Yzma uses this opportunity for a further attack on Kuzco.

When Kuzco begins making fun of many of his classmates, Yzma creates a special soap that will cause Kuzco to look like the things he is making fun of. All of this happening just as the school has to vote on Hutcoming King and Queen. This makes Kuzco upset as he believes he will lose to Ramon.

Kuzco gets detention again. However, knowing the he will enjoy that, Mr. Moleguaco decides to make him join the Overachiever's Club. Meanwhile, Yzma, thinking Kuzco is still in detention, sneaks in there but gets stuck in there when Kronk doesn't recognize her.

Kuzco sits down to read fan letters and finds one saying he should change his show. He does, but receives yet another letter. It turns out it is Yzma trying to use the new shows as a method to destroy Kuzco

When Malina won't pay attention to him, Kuzco uses Yzma's new machine to separate all of her personalities. He then begins to date "Smoochy Malina". However, when she becomes to clingy he dumps her. This causes all of the Malinas to turn on him and now he and Kronk must find a way to turn them all back into one Malina.

By some kind of miracle, Kuzco gets all A's on his report card, while Chaca gets all D's. This leads to Kuzco being put in the SD class where he immediately begins to fail miserably in all of the little games the class plays. Meanwhile, Yzma has received some new potions that flip things around giving the opposite of what is already there. However, before she can use it, the potion switches the floor and ceiling causing her and Kronk to become stuck on the ceiling.

Yzma is cleaning up her old potions and wants to throw them into the river. Kronk tries to prevent this and make her recycle. However, she tricks him and they end up in the river. This begins turning all of the townspeople into various animals. Meanwhile, Malina is trying to make the school paper more interesting so she can get into KuzCollege, and she may have just found her biggest story yet.

When Malina refuses to go out with him yet again, Kuzco decides that since she likes Dirk Brock so much, he will become a rock star so she will date him. However, he becomes a huge jerk and forgets all about Malina. He plans to have a huge concert called "Kuzcokazooza". However, since he is not very good no one plans to show up.