When Mikan's best friend Hotaru transfers to the mysterious Alice Academy, a worried Mikan follows her. Upon arriving she is met by a teacher who explains the only way Mikan can see Hotaru is to become a student. Without hesitation Mikan agrees, knowing once she's enrolled she can never leave.

Mikan is accepted into Alice Academy and can finally see Hotaru again. Upon meeting her peers she is shocked to discover everyone in the school has a special power, which is also known as having a special Alice.

Mikan learns that Alices are valued by the world. Alice Academy was designed to train these elite few and 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 explains she trusts the teacher who told her she has 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 as his Alice allows him to tame animals. 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 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 she has the nullification Alice. However, after upsetting a teacher, Mikan is given the lowest ranking of the school: a no star. This means Mikan will now have to live with the worst of everything including food, dorm, and chores.

Mikan feels her Alice is useless compared to her classmates’ cool powers. She is also placed in a special class populated by students with unique Alices. Shortly Mikan meets a boy named Tsubasa, a middle school student who happens to be in the same group as Mikan. After walking to class together they find the group has put together a welcoming party for Mikan who is now overjoyed to have finally met nice students.