Ten-year-old Mikan Sakura is heartbroken when her best friend Hotaru Imai transfers to a distant boarding school in Tokyo and contact between them is cut off, so she runs away alone to find her. She discovers Alice Academy, a hidden school for children born with special powers called Alices, where a teacher named Narumi tells her she has an Alice of her own and enrolls her. Settling in among gifted classmates, Mikan begins to sense that the academy's bright surface hides stricter rules and buried secrets.