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.

Ledo and Chamber go deep sea-diving to exterminate Earth's Hideauze.