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.

Kugel contacts Ledo and instructs him to return to his side. Upon reuniting with him, Ledo learns that Kugel is struck with some disease that does not allow him to leave his cockpit. When Ledo tells him what he learned about the Hideauze, Kugel reveals that he always knew about it, just like the high command of the Gallactic Alliance, and despite that, he insists to fight them, and was all this time organizing a powerful fleet with a militaristic society with that purpose, whose intention is to rally all the humans on Earth under them. Pinion is summoned to Kugel's fleet, and much to his surprise, he is taken there by Lukkage, who is now working under him, and is approached by Kugel's Machine Caliber Striker, who offers him a post as an engineer to develop weapons for the fleet. The rest of his companions is also forced to join Kugel's fleet as well.

Kugel's fleet prepares itself to attack the Gargantia. Ledo tries to dissuade Kugel with no success while Pinion is approached by Lukkage who plans a rebellion at the fleet. Confused about what he should do, Ledo witness the people of the fleet throwing their sick and weak on the water and fearing that the same will be done to Bebel, he decides to confront Kugel by himself. Agreeing with Ledo's decision, Pinion equips Chamber with some extra weapons, while Lukkage and Flange make preparations for the impending uprising. Melty is instructed by Ledo to deliver a message to the Gargantia, but she almost faints by traveling so far by herself and is rescued in the nick of time by Amy. Informed about Kugel's attack, the crew of the Gargantia consider to abandon the fleet as Ledo suggested, but Amy insists that they should do something to help Ledo as well, and Oldham instructs Ridget to make use of the special key Fairlock entrusted her.