In the gigantic, prestigious missionary school Fuka Gakuen, rumors circulate that the grounds are haunted by mysterious monsters known as Orphans. In order to confront them, the chairperson of the school, brings together a group of girls called HiME who have special powers. Mai Tokiha is one of these HiME. When certain events lead to the awakening of the special abilities within her, Mai devotes herself to the fight in order to protect someone dear to her.