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.

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.