Makoto Niwa is a high school boy who, since his parents are away on business, lives with his aunt’s family. It is there he meets his mysterious cousin of the same age Erio Touwa—who happens to tie a futon around her upper body and is a self-proclaimed alien. Her staple food is pizza. Erio had been missing for half a year and was found floating in the sea. She doesn't remember anything about what happened during that period of time, but she began to think that it was the act of an alien and wanders the neighbourhood wrapped in the futon.
Hino Akiharu lost his parents when he was small and was adopted into his uncle's family. But he noticed his uncle is after the inheritance of his parents, so he decides to enter a boarding school, Hakureiryou high school. However his delinquent boy-like appearance frightens the girls, who make up the majority of the students. Being unable to get along with the classmates, Akiharu meets his childhood girlfriend Saikyou Tomomi.
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.
WIXOSS is a card game that's popular with teenagers. Supposedly there exist "LRIG Cards," female character cards with wills of their own. Special girls can hear the voices of the LRIGs, and those who possess them are called "Selectors." These Selectors have card battles in a dimension that other humans cannot access. It's said that whoever triumphs in these battles will have their wish granted. Ruko Kominato is the latest girl to find a LRIG card. She names hers Tama, and without any further explanation is thrown into her life as a Selector.