In 2167, a radiation wave from the supernova of the nearby star Hydrus Beta inflicted catastrophic damage on Earth, killing millions. It is now 2356. United in rebuilding Earth, humanity prepares for the supernova's second wave of destruction. To shield the planet from future harm, massive space colonies known as "Foundations" have been constructed throughout the Solar System. Serving as hubs for both knowledge and exploration, it is at one of these Foundations—Stellvia—that Shima Katase applies to become a preparatory student, defying her mother's wishes, with the aspiration to see space with her own eyes. At Stellvia, Katase trains to become a pilot and hopes to be chosen for the "Great Mission" to protect Earth from the second wave. While she struggles with both her pilot classes and her turbulent social life, she gradually grows into someone who might just be able to protect humanity.