My-HiME follows Mai Tokiha as she arrives at Fuuka Academy by ferry with her sickly younger brother, Takumi, and is drawn into a hidden conflict after she spots a girl adrift on the water. What begins as a rescue quickly turns violent when an assailant appears, summons a mechanical monster, and forces the injured girl, Mikoto Minagi, to fight back with a supernatural sword. The encounter exposes Mai to a world where the academy is only the surface of something far more dangerous.
Mai soon learns that Fuuka Academy is tied to the power of the HiME, or Highly-advanced Materializing Equipment: female students chosen to defend the academy and the nearby city from the monstrous Orphans. As strange incidents escalate across the school, Mai discovers that she is a HiME too and can summon a Child, a mechanical creature with formidable firepower. Thrust into battles she does not fully understand, Mai joins 12 other HiME in protecting the school, the city, and the people closest to them while trying to uncover the force behind the Orphans.