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.

While waiting to be seated at a restaurant, Kuzco discovers Malina's competitive side. A waiter fills them in on a potato growing contest. Malina enters the contest, but can not grow a potato, so Kuzco offers her some of Yzma's super grow potion. Meanwhile, Yzma and Kronk try to think of new ways the destroy Kuzco, including bringing a statue of him to life.

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.

Kuzco and Pacha's family goes on vacation to the beach. When Kuzco thinks they are taking away his coolness, he starts hanging out with a girl named Yasmine, who just happens to be a young Yzma in disguise.

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

Yzma hires a new foreign exchange student to replace Kronk in her efforts to get rid of Kuzco. Then, he begins to steal of all Kuzco's "popularity". Kuzco and Kronk decide to get rid of Ramon by throwing him into a pit with a wild animal.

Kuzco decides to made a video about Mr. Moleguaco. He enlists Guaca to help him make the video. Soon the video turns into a mess for Kuzco when he insults Guaca, who thinks Kuzco is his new best friend.

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.

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.

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.

Yzma is to be interviewed by Empress Magazine, and will also give a tour of the palace. However, she must somehow distract everyone. She \"invents\" the TV and has Kronk become a TV Superstar to have people become couch potatoes while she does the interview. Meanwhile, Kuzco gets jealous of Kronk getting all the attention.

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.

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.

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?

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.

It is prank day at the school, and Kronk is trying to avoid Kuzco so that he doesn't fall into another one of his pranks. However Kuzco comes to school acting extremely scared of a "Moon Beast" that he saw the previous night.

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.

When Kuzco enters a pep rally, he is disappointed to find out that everyone could care less about him, and they only want to see the school’s mascot, Victor the Llama. In order to gain more attention, he decides to get rid of Victor. Meanwhile, Yzma is getting prepared for her high school reunion, and is having doubts about going because of the kids who made fun of her.

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.

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.

When Kuzco complains about going to Kuzco Academy, Mr. Purutu suggests that he does home schooling. Seeing this as his greatest opportunity, he agrees to it. Yzma realizes that she can't get rid of him in he is home schooled, so she decides to use Malina as the bait to get him back by making Ramon her partner on the school trip. Chicha then starts teaching him 24-7, which forces him to want to go back to school, and so he can stop Malina from being with Ramon.

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.

Giftmas is just around the corner and everyone is getting ready for the holiday. Malina and Yata go shopping to find Kuzco some kind of gift he might actually like, while Pacha tells Chaca and Tipo a bedtime story about Papa Santos. However, Kuzco tells them that he does not exist, which fuels Tipo to find proof that he does. Meanwhile, Yzma’s fruitcake plan fails and she comes up with another way to get rid of Kuzco. She makes a game show about him (which he ironically comes in second place) in order for him to win a trip to a ski resort on Mount Reeve. However, the mountain does not have a resort and Kuzco and Kronk end up frozen. Then some gnomes show up and take the two of them to Papa Santos’ ice palace. Kuzco finally believes in him and finds out that he is on the naughty list, which is why his wishes never come true. He then sets out to correct all the wrong things he has done in order to get his wish to be Emperor. Meanwhile, Malina still struggles on what to get Kuzco.

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.

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.

Kuzco is sick of Kronk getting all the attention, so he decides to join the Inca Ball team. However, his personality clashes with his teammates as Kuzco thinks he can win the game all by himself. This causes him to become a ball hog, so the Kuzco Academy team begins to lose every game. When the final, most important game of the season comes around, the entire team quits, and leaves Kuzco to play by himself.