Mikan Sakura and Hotaru Imai are inseparable best friends, even though it appears the latter does not share the same feelings. Mikan naively assumes her aloof best friend will always remain by her side, until Hotaru decides to leave for Tokyo to attend Alice Academy. The school houses gifted children who possess unique abilities called Alices. Heartbroken and feeling abandoned, Mikan runs away from home to chase after her friend, hoping she can also enroll in the prestigious institution. After Mikan is accepted as a student at Alice Academy and reunites with her friend, she soon discovers that the academy is not all fun and games. The school operates on a hierarchy system based on the strength of their Alice, behavior, and academic performance, while also classifying each student under a specific Alice subgroup for more personalized education. Finding herself in the lowest rank, Mikan faces bullying from classmates who believe she does not belong. Natsume Hyuuga, one of the academy's highest-ranking students, is especially vitriolic toward Mikan for seemingly no reason. The students begin to uncover that the special academy holds hidden secrets—many of which are far darker than one might expect. As they unravel these mysteries, Mikan and her friends find themselves entangled in something much larger than they could have imagined.