Alice Academy is the story of a 10-year old girl, Mikan Sakura, who is devastated when her best friend, Hotaru Imai, transfers to a special school for "genius" kids in Tokyo. After hearing horrible rumors of what happens in the Academy, Mikan runs away from home to seek out her dear friend, and finds that the school Hotaru transferred to, Alice Academy, is specifically for children who each have a special power called an "Alice".

After a teacher at Alice Academy, Narumi, discovers that Mikan has a unique Alice, she is admitted into the school. The story is primarily about Mikan and her experiences at the academy, from the everyday bore of classes and exams to the unexpected clashes with the AAO, or Anti-Alice Organization. Despite her initial view of the so-called greatness of the school, Mikan slowly finds out that beneath the grand facade of the Academy lies a never ending stream of lies and deception.

Also, in the school Mikan meets a boy named Natsume who she at the very start of the manga hates but eventually starts falling for. Along with the many other friends she comes to make such as Ruka Nogi, Yū Tobita a.k.a. Iinchō, and many others. Mikan comes to love the Academy and its teachers despite the truth that is built upon half-truths and lies.

-ANN