When her best friend Hotaru Imai is whisked away to a mysterious boarding school, ten-year-old Mikan Sakura follows her to Tokyo and stumbles into Alice Academy, a school for children born with special powers called Alices. Mikan turns out to have the Nullification Alice, which cancels other students' abilities nearby, and teacher Narumi enrolls her. She settles in among classmates while sensing the academy hides more than it shows.