Kugel and Striker get stranded on Earth following a battle against the Hideauze in space; a young girl named Linaria is pursued by her sisters, who intend to dispose of her; Linaria comes to believe that Kugel is a god.
Striker makes claims; Ledo decides to merge his nerve system with Chamber's interface to increase its capabilities, but at the cost of his life; Ridget bombards the enemy fleet; Striker decides to attack the Gargantia.
Kugel's fleet prepares to attack the Gargantia; Lukkage plans a rebellion; Pinion equips Chamber with extra weapons while Lukkage and Flange make preparations for the impending uprising; Ledo instructs Melty to deliver a message to the Gargantia.
Kugel contacts Ledo and instructs him to return to his side; Ledo learns that Kugel has a mysterious disease; Pinion is summoned to Kugel's fleet; and Kugel discloses the next step of his plan, a large-scale operation that involves the Gargantia.
Pinion and his crew salvage ancient technology but refuse to share it with the rest of mankind; Pinion's fleet does battle with a hostile pirate crew; Ledo questions if he should continue fighting the Hideauze; Chamber informs Ledo about a transmission.
Ledo launches an offensive on a whalesquid nest and is assisted by Pinion's crew; Ledo investigates an ancient facility and makes a stunning discovery; Chamber kills a Hidauze without Ledo's permission.
Fairlock does not resist an attack and nominates Ridget as his successor. Meanwhile, Chamber informs Ledo that he pinpointed the location of their civilization in space; dissident ships follow Pinion's plan and prepare to separate from the Gargantia.
Ledo squares off against a sea creature. Elsewhere, Pinion plans to draft Ledo into his crew with the intention of exploring uncharted territory; Pinion possesses an ulterior motive; Ledo is determined to exterminate all the whalesquids.
Ledo decides to work as a fisherman; Pinion offers Ledo a position on his crew, but Bellows also offers him a post on her salvage team; Ledo and Amy inch closer together; and Ledo confronts an underwater creature.
Ledo must pay for all the damage he and Chamber caused; Lido gives a Hideauze claw to Amy; Dr. Oldham casts light on mankind's old technology and how the Gargantia can't help him return to space; Ledo replenishes the ship's fresh water supply.
Amy gets angry at Ledo for killing pirates, and the leaders of Gargantia discuss the retaliation they may suffer; pirate leader Lukkage launches an attack on the Gargantia, and Ledo agrees to help again in exchange for being accepted aboard the fleet.
Ledo is pinned to a pylon and attempts to open dialogue with the crew, and Amy casts light on the situation. Meanwhile, Ridget, the commander, seeks items of advanced technology; Bellows' ship is attacked by pirates; Ledo attempts to earn trust.
War rages between the Galactic Alliance of Humanity and the threatening Hideauze, and Ledo and his AI robot join in the attack. When a retreat order is issued, Ledo is cast out into space and discovers he's on a habitable planet.