Ayumu Aikawa must continue to fight the Megalo in place of Haruna, who continues to recharge her magical powers. While trying to figure out the mysteries behind the people who are releasing these Megalo in the world, Ayumu meets a beautiful, black-haired girl by chance, and she only has eyes... For his butt.
Tokiha Mai and her sickly younger brother, Takumi, have received a scholarship to attend the prestigious Fuuka Academy. On the way, the ferry they are travelling on becomes the site of a destructive battle between two girls wielding apparently supernatural powers. This is only the beginning of their troubles, as Mai learns that she herself possesses these powers - the powers of a HiME.