Gargantia on the Verdurous Planet

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. Ensign Ledo and his artificial intelligence robot partner, Chamber, join the latest attack against the Hideauze. The attack eventually ends in failure and a retreat order is issued, but Ledo is unable to return and is cast out into space. Six months later, the salvage ship Gargantia retrieves Chamber from bottom of the ocean, 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 Ledo is soon chased and kidnaps one of the crew, Amy. He is chased outside and finds 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 on the pylon. He asks the crew 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 Ledo 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 of advanced technology, Ridget sends Bellows to the point where Chamber and Ledo were found, and Bellows' 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 kill the pirates with no harm to Bellows' ship and crew, as Amy and the others watch in shock at Chamber's destructive power.

After killing the pirates, Ledo is lectured by Amy for his actions and the leaders of Gargantia discuss the eventual retaliation they may suffer from them. Meanwhile, a survivor of Ledo's attack informs the pirate leader Lukkage about it and she decides to launch an attack on the Gargantia. Bellows brings Amy to talk with Ledo, and they explain to him that weapons must be used only as a last resort, as in their world, people must rely on each other to survive. After Amy reconciles with Ledo, a large pirate fleet led by Lukkage is seen approaching the Gargantia. Ledo discusses the situation with Ridget and agrees to help them once more, in exchange for being accepted aboard the fleet. Instructed to defeat the enemies with no casualties, Ledo disables the pirate ships in the front lines and returns to the Gargantia to deal with a sneak attack led by Lukkage herself, piloting her custom yumboro, the "Surfing Lobster". Ledo battles and easily defeats Lukkage, forcing the pirates to flee. Upon being saluted by the crew of the Gargantia, Ledo is greeted by Amy and replies with the first native expression he learned: "Thank You".

After thwarting Lukkage's sneak attack, Ledo receives an invoice to pay for the collateral damage caused by him and Chamber, although Ridget says that he shall be relieved from the living expenses and the fee of having Chamber aboard for his help. While Chamber helps the other workers, Ledo keeps sculpting the Hideauze claw he always carries with him, and when Amy asks him about it, he gives it to her, and she decides to pass it to her little brother Bevel. With Ledo asking for more information about his whereabouts, Amy decides to take him to Dr. Oldham, who explains to him that most of mankind's old technology is lost, thus there is no way for the Gargantia to help him return to space. Some time later, it starts raining, and Ledo helps collect rainwater to replenish the fleet's fresh water supply. Amy takes Ledo to meet Bevel, who asks Ledo about his life in space and the object he was carving. Ledo states that he does not know what it really is; upon realizing that it is actually a flute, Bevel plays it, helping Ledo to recall a long forgotten memory that makes him cry. Ledo then asks Bevel to return the flute to him, and wonders if he should learn more about their surroundings, while Chamber mentions that he must eventually leave it all behind when returning to his unit.

Although Chamber states that he must remain on standby until reestablishing contact with his superiors, Ledo decides to look for a job, but he fails to find a vacant post up to his skills, or willingness. Soon after, the Gargantia stops moving for maintenance, taking advantage of the absence of winds or waves, in an event known as "calm day", with all workers having a free day except repairmen. Despite being a repairman himself, Pinion invites Ledo and Amy, along with her fellow couriers Melty and Saya, for a swim. However, Pinion finds himself unable to cook due to an energy shortage, and sends Ledo on an errand while looking for a way to solve it, while other members of the fleet arrive to join them. Amy and her friends aretasked with an errand to the top of a high tower and they take the opportunity to make it a race. During the race, Amy saves Ledo from being pursued by some transvestite men who intend to hire him, and after the girls' job is finished, they return to the party with Ledo arriving soon after bringing the item Pinion asked him to fetch: a bottle of sauce. Ledo is then informed that Pinion arranged the party to cheer him up, as he did not manage to find a job, and enjoys it with them until the wind resumes and the calm day ends. Amy then accompanies Ledo as he resumes his search for work.

Ledo decides to work as a fisherman, but he finds himself unable to pilot a regular yumboro and sends Chamber to assist the other fishermen instead. Pinion then invites Ledo for lunch and offers him a position on his crew, but Bellows appears and also offers him a jobon 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 obtain a nice catch. Later that night, Amy spends some time alone with Ledo, and the pair become closer. A natural ocean lighting puts Ledo in state of alert and he arms himself to defend Amy, until she calms him down and dances for him upon his request. In the following day, Ledo does salvage work with Bellows and things go smoothly until an underwater creature appears, and with Chamber identifying it as a Hideauze, Ledo abandons his work to confront it.

Despite Bellows' pleas, Ledo kills the creature, a whalesquid (クジライカ kujiraika), considered a sacred animal by the Earthlings, and news of its death spread rumors of an impending misfortune towards the Gargantia. While Ledo has Chamber analyze a sample of it, he wonders why it does not attack Humans on sight like the Hideauze usually do and Chamber deduces that somehow both species learned to coexist. Elsewhere, Pinion plans to draft Ledo into his crew with the intention to explore the uncharted whalesquid territory and salvage its treasures, but Bellows tries to dissuade him, and it is revealed that Pinion's ulterior motive is to enact revenge for his deceased older brother, who was killed by them. As Chamber's analysis prove that the whalesquids are indeed similar to the Hideauze, Ledo is determined to exterminate them all, despite Amy and the others' attempts to make him change his mind. When a huge number of whalesquids are seen approaching the Gargantia, Commander Fairlock declares that all of the fleet's machinery and lights must be turned down, to not provoke the creatures as they pass under them. Amy tries to stop Ledo from fighting them, but he does not listen to her, until Ridget points a gun at him, and he is forced to stand down. The whalesquids pass under the Gargantia without any incidents, but while Ledo rejects Amy for not agreeing with him, Fairlock is informed by Pinion of his plan and Flange declares his intention to accompany him with his ship. As both express their intention to secede from the Gargantia, Fairlock tries to dissuade them until he suffers a heart attack.

Before his death, Fairlock nominates Ridget as his successor. Meanwhile, Chamber informs Ledo that he finally managed to pinpoint the location of their civilization in space, but their current location is too far from it, and it may take thousands of years until someone picks up their distress signal. As Fairlock's funeral is held, several dissident ships agree to follow Pinion's plan and prepare themselves to get separated from the Gargantia. Melty decides to leave with them, and Saya asks Amy if she does not want to leave with Ledo as well, but she responds that she can't abandon her brother. Seeing how much his sister is suffering with Ledo's decision to leave, Bevel tries to dissuade him, and Ledo says that his drive to kill the whalesquids also comes from his desire to protect both Amy and him from the Hideauze. Instead of attending her foster father's funeral, Ridget looks for a solution to stop the fleet from splitting up, but Bellows reminds her that she does not need to take all the burden to herself, as she will always have the rest of the fleet to support her. Ridget then sees Fairlock off as his body is sent to the waters and asks the members of Gargantia to lend her their support. Soon after, a devastated Amy watches as the dissident ships leave the Gargantia, with Ledo aboard them.

Ledo starts his offensive on the whalesquid nest, assisted by Pinion's crew and their barrage of depth charges, obliterating the enemies without much effort. While investigating an ancient facility, Ledo finds some records and upon accessing them, he learns that the Hideauze were once humans who underwent heavy genetic modification to adapt themselves to space environment, calling themselves "Evolvers". Viewing their efforts as blasphemy, a faction of mankind declared war on them, leading to their current conflict after both sides abandoned Earth during the fifth ice age, except for the ancestors to the current humans and whalesquid living on the planet. Devastated by this revelation, Ledo shouts in despair when Chamber slays a Hideauze (human sized) child without his permission. Back at the Gargantia, both Bevel and Amy show signs of how much they miss Ledo.

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 says 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. Meanwhile, Ledo hears from Chamber that the lightbugs that mankind use as a power source were also created by the Hideauze, which further proves their discovery. Ledo then questions if there is still a need to keep fighting the Hideauze after all they learned. The Machine Caliber replies that it came to the conclusion that the Galactic Alliance and the Hideauze are too different for them to coexist, as one side evolved and perfected their civilization while the other relinquished civilization altogether, thus their conflict is inevitable. Chamber then informs Ledo about a transmission from a Galactic Alliance vessel and as a huge fleet approaches them, Ledo sees Commander Kugel's Machine Caliber atop it and finds that he is alive.

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 Galactic Alliance, and despite that, he insists to fight them, and was all this time organizing a powerful fleet with a militaristic society for 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 Kugel, 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 are also forced to join Kugel's fleet. Some time later, Kugel discusses with Ledo the next step of his plan: a large scale operation which, much to Ledo's shock, somehow involves the Gargantia.

Kugel's fleet prepares itself to attack the Gargantia. Ledo tries to dissuade Kugel with no success, while Pinion is approached by Lukkage who is planning a rebellion at the fleet. Confused about what he should do, Ledo witness the people of the fleet throwing their sick and weak into the water; realizing that the same will be done to Bevel, he decides to confront Kugel by himself. Accepting 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 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. The rebellion begins, and while Ledo fights Kugel assisted by Pinion's crew, the pirates led by Lukkage attack the fleet's soldiers. When Ledo finally manages to pin down Kugel and open Striker's cockpit, it is revealed that Kugel was long dead inside it.

Striker says 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 Striker 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 nervous system with Chamber's interface to increase its capabilities at the cost of his life. However, Amy appears soon after to tell Ledo that he does not need to fight alone. Meanwhile at the Gargantia, Ridget uses the key she received from the Fleet's former commander to activate an ancient mass driver stored inside the main ship, and uses it to bombard the enemy fleet. Pinion evacuates his crew aboard the salvage vessel, and intends to destroy both the recovered relics and Striker's followers attacking his ship, but is saved at the last second by Lukkage. Striker then decides to attack the Gargantia but Ledo and Chamber pursue it. Despite being willing to sacrifice his life to protect his friends, Ledo reveals that his true desire is to survive the battle and return to live at the Gargantia with Amy. Chamber then relieves Ledo from duty and ejects him to safety before destroying Striker in a suicide attack. Some time later, Lukkage and many survivors of Kugel's fleet join the Gargantia. Ledo has become an experienced salvager who seeks to understand the whalesquid, and is able to enter their territory without provoking them. He hopes that humans will eventually learn the means to properly communicate with the creatures. He also seems to be in a relationship with Amy. In the ocean, a whalesquid larva is attached to Chamber.