Mikan Sakura grew raised in the Japanese countryside with her grandfather. Mikan decides to accompany her best friend, Hotaru Imai, to a famous Tokyo high school. The school is actually an exclusive Academy for brilliant individuals with "Alices," a special skill that varies from person to person. Mikan meets an Alice instructor named Narumi at the school's gates, is admitted as a result of a chain of circumstances, and is informed that she carries an unique Alice. Mikan gradually realizes that underneath the majestic exterior of the Academy, there is a never-ending stream of falsehoods and buried truths, despite her initial impression of the school's alleged superiority. The school's increasingly manipulative and nasty behavior toward her makes it difficult for her to feel safe.