Ichika Orimura is attending the Infinite Stratos Academy as he is the first male in the world to ever pilot an IS where he becomes a sensation among the all female students of the academy. With his homeroom teacher being his older sister Chifuyu, an ex-IS pilot, Ichika is in unease and unprepared and trying to get used to the academy. Later he learns his dorm roommate is his childhood friend, kendo champion Houki Shinonono, who he has not seen in six years. When his class decides to elect him as their class representative, the British cadet representative and noble, Cecilia Alcott is against it and challenges him to an IS duel for the position.