Étudiant de 20 ans, Minato Sahashi a un très gros manque de confiance en lui et échoue très souvent à l'examen d'entré à l'université ! Mais sa vie banale et ennuyante va vite se terminer quand une Sekirei nommée Musubi tombe du ciel... Elle lui informe qu'il est maintenant son Ashikabi, une personne associé à une Sekirei. Minato devra alors s'associer avec Musubi pour reprendre une vie normale.

Since the ancient times, the Kannagi priestesses have used their swords, or Okatana, to exorcise the creatures known as Aratama that brought chaos upon the world of man. These maidens were known as Tojis, a special task force within the police allowed to have their Okatana on their person because they are government officials, but they mostly consist of school girls who go to one of five training schools. This spring, the top Tojis from five schools across the country have been gathered for a customary tournament where they will use their abilities and fight for the top position.

In a prosperous city named Russell City, an omen that threatens to shake its world begins to move within it. A man named Sword is the first to hear the first stirrings of the plot, and throws himself into a shadow war in order to expose it. His only clue is the key word "El Dorado." He meets Sophie, a woman searching for her missing older brother who has only left her with the same words: "El Dorado." With Sword having also lost his younger sister in the past, both are drawn together by the words, and work together to find out its meaning.