In a remote era, far within the reaches of the universe, humanity is in a life-and-death struggle against the repulsive Hidiaazu species as a member of the Galactic Alliance. Lieutenant Ledo and his humanoid weapon, Chamber, are pulled into a mysterious vortex during a vicious conflict. When Ledo awakens from cryogenic stasis, he finds himself marooned on a lost Earth deep underwater. The inhabitants of this submerged world survive by living on giant ships and searching underwater ruins for resources. Ledo partners with a young courier, Amy, and joins the survivors of the Gargantia fleet. He learns to adapt to a new way of life that dismisses knowledge of Earth's past and culture, and must also adjust to a peaceful existence that contrasts sharply with everything he once knew.