Gargantia on the Verdurous Planet

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.