When Mikan's best friend Hotaru transfers to the mysterious Alice Academy a worried Mikan follows her. When she arrives she meets a teacher at the school, Narumi, who tells her the only way for her to see Hotaru is to become a student of the school. Without hesitation Mikan agrees and thus begins her life at Alice Academy!

Mikan is accepted into Alice Academy and can finally see Hotaru again. She also meets the other people in her class and gets a huge shock when she finds out that everyone in the school has a special power or Alice.

Mikan learns that everyone in Alice Academy has an Alice and that people with Alices are valued by the world. Alice Academy was designed to train these "elites" and so only those with Alices are allowed in the school. When the class finds out that Mikan doesn't know her own Alice they start to bully her but Mikan stands up to them and says that she trusts Narumi who told her she had an Alice. Natsume then challenges her: if she can survive going through the North Forest then he and the rest of class will accept her.

In the North Forest Mikan, Hotaru, and Iincho get trapped by a violent Teddy Bear, and a giant chick. The group forces Ruka to help them as his Alice allows him to tame animals including the giant chick. When Natsume hears that his best friend has been forced to help, he gets angry and tries to burn Mikan with his fire Alice. Before he can do it though a bright blue light engulfs everything and Natsume is unable to use his powers. Could this be Mikan's Alice?

Mikan has finally been accepted by her classmates after discovering that she has the nullification Alice. However after getting on the wrong side of a teacher Mikan is given the lowest ranking of the school: a no star. This means that Mikan will now have to live with the worst of everything including food, dorm, and chores.

Mikan begins to feel that her Alice is useless compared to her classmates cool Alices. The day arrives for the elementary students and the middle school students to have a combined lesson. Mikan learns that she is in the special class which is populated by those who Alices don't fit into the other groups. After getting into trouble with some older students Mikan is rescued by Tsubasa a middle school student. When he finds out that Mikan and he are in the same group he takes Mikan to their classroom. There they find that the group has put together a welcoming party for Mikan. Mikan is very happy to find out that there are a lot of nice students in her group and that she has a place where she belongs.

Natsume and his gang keep ditching class. Mikan makes a bet with Natsume that if she wins in a dodgeball game he and his friends will stop skipping class. Natsume agrees but if Mikan looses then she must do whatever he says. The game begins but with a twist: unlike regular dodgeball in this game people can use their Alices through the dodgeball!

Whenever Mikan writes a letter to her Grandfather, she gives it to Narumi who she believes is sending them to her Grandfather. However Mikan soon finds out that Narumi has not been sending them and instead has been hiding them in his desk drawer. An upset Mikan escapes from the Academy to go see her Grandfather. Some men try to kidnap her after finding out that she's from the Academy but luckily Narumi arrives in time to save her. Narumi gets shot while rescuing her which causes Mikan to get upset that she has put her teacher in danger. She agrees to go back to the Academy with Narumi after seeing that he's not such a bad guy after all.

Hotaru is up for an honor student prize against an older student. Whoever wins in a robot fighting match will get the prize. Another robot that Hotaru built to resemble Mikan, Amanatsu, wants to help. The robot is sad when Hotaru tells her she doesn't need her help so Mikan tries to find other things that Amanatsu can do to help Hotaru. All efforts to help end in failure but then Mikan and Amanatsu hear that the older student is going to cheat in the match. Amanatsu enters the match to stop him and ends up finally being able to help her beloved Hotaru.

All of the students get an allowance and one day they decide to go to the campus's Central Town, the mall for Alice Academy students. Everything sold there is made by Alices so Mikan is excited to see it. The teacher Jinno forbids her to go to Central Town unless she is accompanied by her partner Natsume. Luckily for Mikan Natsume is taking care of a little boy named Yoichi who is in the same group as him and Yoichi also wants to go to Central Town. Because Natsume has a soft side for the kid he agrees and they all go to Central town. Once there Mikan spends her money to set a talking apple free and is unable to buy the town's famous cotton candy. Mikan then earns the money to buy a small box and end up sharing it with everyone including Natsume.

Mikan's dorm catches on fire and all of the students use there Alices to help put it out. Including Mikan who tries to save a little kid's prized possession. The fire brings back unpleasant memories to Natsume about his life. Mikan's group teacher Noda who has the time traveling Alice arrives back in his time and decided to give Mikan a lesson. The lesson end's with Noda telling Mikan to keep practicing her Alice. After failing to cancel other people's Alices, except for the one time when she saves Hotaru from her teacher's Alice, Mikan learns that her Alice only works when she wants to protect someone. Noda tells Narumi what he saw in the past causing Narumi to realize something.

The school festival has begun! It will last for two weeks ending with a dance. The four groups will each participate and the one that has the best performance will win an award. Mikan's group isn't interested in participating mainly due to the fact that non of there Alices have anything in common like the other groups. Mikan trys to come up with an idea and comes up with the idea of a role playing game with help from Natsume. It takes a lot of effort to get their idea approved but it eventually does. Natsume then passes out from a wound that he got while on a mission for the Academy.

The festival continues. Reo, a graduate of the school and now famous singer, even comes to give a concert. However the big star has other plans besides a concert. His real mission is to kidnap Natsume!

Mikan and Sumire who had witnessed Reo kidnapping Natsume escape from the school to rescue him. They end up being captured as well. Mikan, and Sumire end up in an abandoned warehouse with an unconscious Natsume. Feigning unconsciousness as well Mikan and Sumire find out about the dark secrets of Alice Academy.

Mikan manages to get in contact with the school through the communication device (panda shaped headphones) Hotaru gave her. As Natsume burns through the ropes tying him Narumi gives the three instructions. But Natsume's Alice alerts Reo to their awakening and he takes the device away from them. He has his own conversation with Narumi, and it seems Reo and Narumi were friends at school along with "that person". After he destroys the device Leo sets out to find what type of Alices Mikan and Sumire has. When Mikan isn't affected by his Alice Reo learns that she has the nullification Alice. Leo is shocked and has an investigation done on "that person." After Reo and his men leave Natsume tells the other two to escape. As the two make a run for it Natsume threatens Reo that he will blow up the warehouse if he tries to pursue them. Mikan realizes while running that Natsume isn't bluffing and that he really intends to blow himself up. Mikan runs back and stops Natsume just in time.

The Special type class has set up their RPG maze game for the festival and are ready for costumers! Sadly nobody seems interested until Narumi, Natsume, Ruka, and Sumire come. Ruka, Narumi, and Sumire all fail, but they get other people interested in it, and soon there's a huge line! Natsume provoked by Tsubasa enters the maze and ends up winning. The winner may pick a lamp from the prize table. The lamps belong to each member of the special types class and the person who's lamp is chosen will become the winner's slave. Natsume in order to get revenge on Tsubasa tells Yome to find out which one is his but Yome misunderstands and Natsume ends up with Mikan's lamp.

Mikan joins Natsume and Ruka for the rest of the festival as Natsume's slave. Nothing can really keep Mikan down for long though and she ends up having fun. Mikan of course decides that she has to play Hotaru's robotic chicken game. A little boy sneaks into the game and uses his Alice on his robot which causes it to malfunction. Mikan saves him but is wounded in the process. Everybody thinks its Hotaru's fault because she made a faulty invention but the little boy confesses. A member from the student council, Imai, comes to see whats happening and after hearing this heals Mikan with his alice AND gives the little boy's brother her pain as punishment. About to walk away Imai meets Hotaru who surprises everyone by revealing a relationship between the two.

Ruka explains to Mikan why Natsume acts the way he does. The three end up at the hunted house attraction. They enter the hunted house and Mikan gets scared by everything whether it's scary or not. While running away from a scary old lady Natsume and Mikan get separated from Rukia and worse get trapped in the house by a wall that suddenly appears!

Ruka is starring in the festival's play along with a girl named Yuri. Yuri's Alice is a girl attracting pheromone which she uses to attract a bigger female audience. The twist is Ruka is playing Snow White and Yuri is playing the prince. After an accident which involves Hotaru, a camera, and a sticky substance, Mikan ends up playing the prince and Natsume ends up playing a jungle cat.

The Special Ability class receives an award for their RPG. At the award ceremony Mikan sees the principles for the first time and Narumi decides to give Mikan her grandpas letters. Then it's time for the festival's last dance. Supposedly, the girl and her dancing partner will fall in love forever if they dance the last dance together. Every girl in school wants Natsume or Ruka to be their partner for the last dance of course. But both Natsume and Ruka want to dance with an oblivious Mikan.

Its exam time at Alice Academy, and those who do well are rewarded. The person who gets the top marks will be rewarded with a trip back to their family and a Central Town shopping ticket. The prospect of seeing her Grandpa gets Mikan all fired up and she studies really hard. Her enthusiasm rubs off on the other students and they all start studying too.

Kaname who has the Alice of putting souls into dolls visits the school from the hospital for one week. He created Mr. Bear when he was little and during his stay at school he creates more dolls for his classmates. However using his Alice comes at a price.

The circus has come to Alice Academy for Academy Day. Mikan is moved by the circus and starts preaching to everybody that they should work hard without using their Alice. Ruka who is concerned for the mistreated animals at the circus goes to visit them. While there he is cornered by the ringleader who is actually Reo.

The students rebel when Natsume is forced to go on another mission. Narumi, threatened by Persona, pretends to offer his help to the students but tricks them instead. This causes the students to get angrier and they rebel even further.

Reo sends his own crew to help the students rebel. Upon finding out that Reo was behind everything the students change sides and work together with the teachers to bring Reo down.

Mikan fails her finals and has to take makeups. While stressing about what will happen to her if she fails the makeups, Mikan finds out that Hotaru is transferring after graduation. After talking to Natsume, Mikan decides to let Hotaru go. Then when Hotaru leaves without saying goodbye to Mikan the whole class chases after her. Mikan arrives and tells Hotaru that she has decided to stop following her but that she will be her friend forever.