The story takes place on a planet different from the Earth. They call their planet the Great Air Continent. There, they are born as female. When they become 19 years old, they go to the "spring" and choose their sex to become "adult".

They are at war; the country where the main characters live is invaded by the next country aiming at their superior engine. Day by day, the situation is getting severer. To intercept their attack, they convert the two-seater plane for ceremony, Simoun, into a fighter. Also, they organize an air squad, "Call", which consists of "Mediums". They are girls who don’t decide their sex yet.

The girl who can operate "Simoun" is called "Simoun Siwula". Because they have special abilities, they can choose when they become “adult” by themselves. However, since the war broke out, they've been forced to continue to be pilots, i.e., "girls".