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.

Amy tries to help Ledo find a job and introduces him to a number of different industries aboard Gargantia, but he's just not able to land one. Then the wind dies down and the waves cease, making it a "Calm Day", during which time the fleet shuts down so a lot of repair work can be done. But for non-repair-related personnel, it's time to take a breather. Pinion invites Ledo, Amy and her friends to a BBQ party. Everything seems to be going smoothly...

Ledo decides to work as a fisherman, but he finds himself unable to pilot a regular Yunboro and sends Chamber to assist the other fishermen instead. Pinion then invites Ledo for lunch and offers him a position at his crew, but Bellows appears and also offers him a job at her salvage team. In the occasion, Amy and her friends dance to the crowd and Ledo mistakes a cooked octopus for a Hideauze and is about to shoot it until the others assure him that it is not an enemy, but food instead. Chamber, who finds himself causing a mess among the fishermen asks for Ledo's help and he uses his mecha to properly help the workers have a nice catch. Later in the night, Amy spends some time alone with Ledo, and a lighting puts him in state of alert and he arms himself to defend her, until she calms him down and dances to him upon his request.

When Ledo has an encounter with a whalesquid undersea, he attacks and kills it because of its similar appearance to the Hideauze. Little did he know that whalesquid are considered sacred, so murdering one is taboo, and soon the whole ship is in an uproar over it. Ledo, however, believes that whalesquid are Hideauze and he's determined to carry out his mission by slaughtering more of them before they decide to target humans on Earth. Just as Amy tries to stop Ledo, a huge pod of whalesquid approaches the fleet...

On his deathbed, Fleet Commander Fairlock entrusts Ridget with Gargantia. Meanwhile, Chamber finally gets a fix on the location of the Galactic Alliance, but they're so far away that Ledo will never be able to get home. As preparations are underway for Fairlock's funeral, Shipmaster Flange announces that he's leaving Gargantia. Ridget struggles to keep other Shipmasters from following suit. Pinion has plans of pillaging the ocean floor, so he joins the like-minded Flange. Amy is sad when two people she cares about are leaving as well, Melty and Ledo...

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

With all the Hideauze in the area killed, Pinion and his crew manage to salvage ancient technology not seen anywhere, but instead of sharing it with the rest of mankind as originally planned, Pinion claims that they have the right to keep it to themselves, and sends a message to the other fleets warning them to keep out of their territory. As the message reaches the Gargantia, the fleet had just reorganized itself and there is the concern that other ships may leave to join Pinion's side as well. With the technology salvaged by them, Pinion's fleet defeats a hostile pirate crew who in return asks for a place among them, and he agrees. Ledo, still in shock upon learning the truth about the Hideauze hears from Chamber that the lightbugs that mankind use as power source were also created by the Hideauze as well which further proves their discovery.

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.

Striker claims that it was following Kugel's instructions after his death and eventually reached the conclusion that to ensure stability to the fleet, it was necessary for the humans to view it as their god. Both Ledo and Chamber reject Striker's offer to join its side and decide to destroy it. Unable to defeat Striker in their current condition, Ledo decides to merge his nerve system with Chamber's interface to increase its capabilites at the cost of his life, but Amy appears soon after to tell him that he does not need to fight alone. Meanwhile at the Gargantia, Ridget uses the key to activate the mass driver stored inside the main ship and uses it to bombard the enemy fleet while Pinion evacuates his crew and intends to take the enemies assaulting his ship with them, but is saved in the last moment by Lukkage. Striker then decides to attack the Gargantia but Ledo and Chamber pursue it.