Throughout history, an elite group of shrine maidens known as "Toji" have saved the world from "Aratama," strange and malevolent beings bent on destroying humanity. In modern times, these warriors have been assigned to a special police squad to exterminate Aratama. The government has also set up five elite schools across the country to provide young girls the necessary sword fighting skills to eradicate these monsters and eventually join their fellow Toji in protecting the world.

A student of one of those five schools, Kanami Etou is chosen to represent Minoseki Academy in a sword fighting tournament, where she meets the mysterious Hiyori Juujou. Although Kanami and Hiyori rise to the top of the tournament, their battle takes an unexpected turn, throwing the world of the Toji into chaos. Likely that the Toji are facing betrayal from within, the two are forced to flee the tournament, clashing with former comrades on the way.