A man arrives in town that claims to be Kuzco's father. Kuzco, who does not remember his father, immediately thinks he is telling the truth and the two becomes inseparable. However, everyone else is suspicious of the man, and it turns out that he might not be who he says he is.

It is Malina's birthday, and she is having a extravagant ceremony called a Bloom Ball to celebrate. Kronk is going to give her a time travel watch, while Kuzco is going to give her pictures of him. Kronk warns Kuzco to not take over and make the party all about him, but that proves useless as he ends up ruining the party. In order to make things right, Kuzco decides to use Kronk's time-travel watch to go back in time and make things right. Meanwhile, Yzma has put a fly potion in the punch so Kuzco will transform into a fly and she can squash him.

Kronk enters a contest to win a picnic with his hero Pajama Llama. Kuzco finds the ticket and agrees to give it to Kronk if he becomes his butler. However, Kuzco does not realize that the ticket has an expiration date until it is too late. Now he must find someway to tell Kronk.

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.

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 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.

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.

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.

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.

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.

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.

Project Poncho is coming to Kuzco Academy and every student must make a poncho for the contest for their assignment. Kuzco desperately wants to win so he can take Malina on a \"romantic getaway\" to Lima, so he tries to steal other people's ponchos. After seeing Guaca's poncho, Kuzco convinces him to let him take it. Meanwhile, Yzma also enters the contest, and asks for the help of two silk worms to help her. However, when she refuses to pay, they decide to make a fool out of her.

The school is holding elections for a new class Vice-President. Mr. Moleguaco tells Kuzco if he runs an election and gets elected, he will pass Government. Kuzco them uses a potion to turn himself in Kronk and try and ruin his reputation.

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.

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.

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 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.

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?

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.

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.

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.

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.

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.