Mikan and Hotaru grow up in a small town in the remote countryside. They are close friends. Suddenly, Hotaru moves to a school in a big city. Mikan misses Hotaru so badly that she decides to find her. She follows Hotaru to a school called “Alice Academy,” only to be kicked out as no interview or meetings with students or teachers are permitted at this academy. She finds that only the students gifted with special ability are accepted here. Just then, Mikan has an unexpected chance to get into the school for a one week trial admission thanks to a teacher, Mr. Narumi who senses something special in Mikan.

Mikan is overjoyed to see Hotaru, but soon she has a quarrel with Natume, the boss of the class and faces the spiteful attitude of the other students in the class. Hotaru is of no help to Mikan. Natume and other students suspect Mikan has no special power at all and start to use their Alice on her. But, to their astonishment, Mikan protects herself from their attacks by neutralizing the malicious energy. This is her Alice. One week later Mikan is officially accepted to enter the academy. However, she has no idea what is waiting for her in this paranormal world of Alice Academy. As of yet unknown to her, many strange and wicked plots are secretly going on.