In 2167, a supernova explosion engulfed the Earth with a wave of electromagnetic energy, turning the sky green and causing countless disasters. After recovering from that first wave, humanity started putting up defences to protect itself, and by the year 2356, a network of six orbiting space stations, the Foundations, now guards the Earth from a second supernova wave that is expected to arrive later that year. Each Foundation houses a high school for promising young space cadets, and eager 15-year-old Katase Shima has just been accepted to Stellvia, the second Foundation. Making friends, going to class, learning to pilot a light spacecraft — it is all part of the high school experience, hundreds of miles above Earth aboard space station Stellvia.

In the PlayStation 2 game, the player assumes the role of a new student who has enrolled at the Stellvia Space Station Foundation. Each day he assigns various commands on what to do such as studying or resting in the same type of gameplay that Tokimeki Memorial has except for weekends since there is no school then. At the weekends he may invite a character on a date. There are various events to be seen in the game and there are 10 multiple endings. The game resembles the aforementioned Tokimeki Memorial game series in many ways (though in Tokimeki Memorial the player only assigns various commands for the coming week and not for each day)