Mai Tokiha and her brother Takumi are on a boat trip when a girl with a sword, Mikoto Minagi, is found in the water. They pull her aboard, but are attacked by Natsuki Kuga. The boat is destroyed in the battle between Mikoto and Natsuki, and Mai shows strange abilities.

Mai and Takumi go to their first day at school. Mai skips class and bonds with Mikoto over a bowl of ramen. Takumi is attacked by a monster, and Mai and Natsuki put aside their differences to fight it.

Mai calls forth Kagutsuchi and defeats the Orphan Later, Mashiro Kazahana explains to Mai that she is a HiME and that she is needed to fight Orphans. Mikoto becomes Mai's roommate.