In the distant future, mankind has taken to exploring the stars. From their travels they've established a new utopia called Avalon under the leadership of the Galactic Alliance of Humankind. But even with this newfound paradise, peace still eludes mankind as they're caught in an ongoing struggle with an alien species known as the Hideauze.

Ledo is a soldier of the war, and finds himself stranded on an unfamiliar planet after a disastrous battle. Stuck with no means to contact the Alliance, Ledo is left with no choice but to acclimatize with the humans on Gargantia, a fleet of ships that sail across the forgotten planet Earth. But as he and his new found friends learn about each other's worlds, they're about to uncover a shared connection that has far reaching consequences.