Narumi Fujishima is an ordinary high school boy who remains isolated from his fellow classmates. One afternoon fellow classmate Ayaka Shinozaki invites Narumi to join the gardening club and introduces him to a reclusive detective named Alice. Alice hires Narumi as an assistant and puts him to work solving the strange mysteries of Angel fix, an illegal drug. Little does he know it could put him and Ayaka in serious trouble.
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.