In the year 2167, a wave of radiation released by the supernova of the nearby star Hydrus Beta caused cataclysmic damage on Earth, leaving millions dead. Now, it is the year 2356. United to rebuild Earth, humanity prepares for the supernova's second wave of destruction.

In order to protect the planet from future harm, massive space colonies called "Foundations" have been built throughout the Solar System. Acting as centers for both knowledge and exploration, it is at one of these Foundations—the Stellvia—that Shima Katase applies to be a preparatory student against her mother's wishes, aspiring to see space directly with her own eyes.

At the Stellvia, Katase trains to become a pilot and hopes to be selected for the "Great Mission" to shield Earth from the second wave. While she struggles with both her pilot classes and her tumultuous social life, she slowly grows into someone who might just be able to protect humanity.