A mysterious organization is attempting to raise a ruin from the ocean depths using cyborgs called 'Grand Chers'. When Hime, an ordinary Tokyo girl, establishes a psychic bond with a particularly powerful escaped robot, it precipitates a crisis of faith in 16-year-old Grand Cher pilot Yuu. Their encounter leads Yuu to break with his parents' organization a year later and join Hime in Novis Noah, a group that opposes their goals. The raising that ruin representing a threat to human civilization.