Mikan Sakura grew up with her grandfather on the countryside of Japan. When her best friend, Hotaru, transfers to a prestigious school in Tokyo, Mikan follows her. The school is actually an elite Academy for gifted people with "Alices," an ability that is unique depending on the individual being. Once Mikan arrives to the gates of the school, she encounters an Alice teacher named Narumi, gets enrolled due to a series of events, and is told that she possesses a rare Alice. Despite her initial view of the so-called greatness to the school, Mikan slowly discovers that beneath the grand facade of the Academy, there is a never-ending stream of lies and buried secrets. The school's increasingly manipulative and sinister actions towards her make it a dangerous place to be. Little does Mikan know that her enrollment in Alice Academy set the gears in motion to an even greater tragedy.