Humans have left Earth and have made a paradise in space, Avalon, as humanity's new home and created the Galactic Alliance of Humanity to expand their journey through it. A threat known as Hideauze appeared before the Alliance and a war rages between them. Second Lieutenant Ledo and his A.I. Robot Partner Chamber joins the latest attack against the Hideauze. The attack ultimately ends in failure and a retreat order is issued, but Ledo is unable to return and is cast out into space. 6 months later, the salvage ship Gargantia retrieves Chamber, but are unable to take it apart. After everyone leaves, Ledo decides to take a look around and gather intel on where he is, but is soon chased and kidnaps one of the crew, Amy. He is chased outside to find out he is on a habitable planet, which shocks him enough to release Amy. The crew pins him on a pylon, and he calls Chamber, which the entire crew is surprised to see moving and floating.

Deciding to try and open a dialogue with these people, Ledo stays pinned to the pylon. They ask to talk to the Alliance in charge, but the crew have no idea what he is talking about and they believe that Chamber, who is translating, has another person inside. As Ridget, the commander, and the crew try to decide what to do, Amy gives Red food and begins talking. She explains that this is Earth, and when it was frozen over, some humans escaped to the stars while others stayed. Eventually, the ice melted and became a vast ocean, in which many people form fleets to salvage old technology from below. Looking for other items advanced technology, Ridget sends Bellows to the point where Chamber and Ledo Were found, and her ship is attacked by pirates. Amy asks Ledo to help them, and he agrees with the intention of earning their trust. Ledo boards Chamber and efficiently eliminate all enemies with no harm to Bellows' ship and crew, as Amy and the others watch in awe at its destructive power.

After Chamber wiped out all of the pirates that were threatening Bellows and her people, Ledo is perceived as a menace and kept under guard by the crew of the Gargantia. And perhaps rightfully so, as the pirate armada that is Empress Lukkage's fleet is racing towards the Gargantia Fleet with bloody revenge in mind...

In order to compensate for the damage to the hangar they caused, Chamber is put to work hauling around heavy cargo, but that leaves Ledo on the sidelines with nothing to do. Amy takes him around the fleet and introduces Ledo to the knowledgeable Dr. Oldham as well as her sickly but wise younger brother, Bebel.