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.
Lain Iwakura appears to be an ordinary girl, with almost no experience with computers. Yet the sudden suicide of a schoolmate, and a number of strange occurrences, conspire to pull Lain into the world of the Wired, where she gradually learns that nothing is what it seems to be... not even Lain herself.