AD. 2023, Tokyo. Because of the change of the society such as internationalization and enlargement of the trading, the dark side of the society also continues changing. The criminals are getting deep, and their organizations are increasing its size, then the peace and security is getting worse. The government takes it seriously, and decides to introduce an innovative system. In order to cope with the special criminals, an extralegal police is founded. It is a special criminal team, Warriors, which consists of a few elite members.
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.