Sidonia fires her Super Hyggs Particle Cannon at G542 and, managed to create a very large hole. But the waves caused when firing Super Hyggs Particle Cannon, cause interference with communication signals. The remaining pilots regroup and attempt to break into the enemy placenta.
While the Ren's Garde damaged when the big waves occurs earlier. Nagate who happened there, intending to catch up and join the 1st Platoon alone, because Tsugumori equipped with the latest propulsion. Before Nagate depart, Ren Honoka entrusts him with her last core-piercing projectile, asking him to defeat Benisuzume and avenge Hou's death in her place. Ren then withdraws from the battle, along with damaged unit 314. Izana who happened to see Nagate go, decided to follow him.
Samari and some other pilots will be entered into the G542, at the time Benisuzume appeared and beat them all, but Nagate managed to stop her when he had just come. He asked Samari and the others to go inside the G542 while he is dealing with Benisuzume.
The battle between Benisuzume with Tsugumori and Nagate begin. The attack started from Benisuzume with a spread attack, Nagate managed to avoid although a little surprised by that unfamiliar attack. And the battle between the two continues to be more exciting. Meanwhile, Ittan Samari and other pilot managed to get into the G542.
In Command and Center Room of Sidonia, they detected strange movements of the G542 are trying to form a Hyggs Particle Emitter to shoot Anti-Planetary Missile.
The fight between Benisuzume and Nagate still continued, they threw each Hyggs particle attack. But Nagate under the bad circumstances, because he was pulled by the gravity of the dwarf planet which complicates the movement and also hyggs particle emitter that of the G542 beam fired at him as a form of support to Benisuzume.
Attacked, Tsugumori suffered minor damage, but Nagate in a state of unconsciousness. Nagate will be pulled by the gravity and hit the surface of the dwarf planet. Izana come to save Nagate who had been following the his movements. Although she can save Tsugumori, Izana's Garde overloaded due drawf planet gravitational field and it can explode at any time. But surprisingly, Izana can move away from the G542 and managed to save Nagate.
Benisuzume who come chasing Izana and Nagate, shoot them with Hyggs particle cannon. Shot on target, Izana's Garde suffered minor damage and knocked away from Tsugumori. At the same time, Nagate woke up and resumed his fight with Benisuzume.
10 minutes, Anti-Planetary Missile almost reached the target. During that time, Samari and others pilots dive deeper and deeper into the body G542. Firing hyggs particle cannon to destroy the placenta that form a protective wall. No energy left to go home, Kōichi Tsuruuchi fired his Hyggs particle cannon without hesitation.
Nagate fight against Benisuzume continues, by using the SHS-BAD, Nagate fired CPP towards Benisuzume until he run out of ammunition. Then Nagate remembered with a projectile given by Ren. But unfortunately, his SHS-BAD shot by Benisuzume's Hyggs particle cannon. At that time, Nagate already made up his mind, Benisuzume is not Shizuka Hoshijiro or even human, and in a last ditch effort, Nagate fires Tsugumori's entire left hand, holding the projectile given by Ren, into the Gauna, finally destroying it.
Meanwhile, after pilot Kōichi Tsuruuchi exhausts the last of his Hyggs supply breaking through the last barrier protecting the 'Mother Gauna', the remaining members of Samari's platoon destroy the Gauna's mother core. Carrying Tsuruuchi with them, Samari and Seii escape to safety with the others as the Anti-Planetary Missile obliterates its target.
Izana woke up and found herself rescued by Ren. Figuring all 1st Platoon killed unless they, both of them were surprised when viewed 7 Gardes in formation coming toward them. Pick three other units, all Gardes return to home, to Sidonia.
The Sidonia Government publishes a battle against G542 which led to 38 pilot fall on the battlefield. At the same time, Norio was in his residence, he questioned his mental attitude and this time was very embarrassing. During that time, Nagate came to his home, asked about the truth of Norio resignation, and despite being unable to forgive him, expresses his desire to fight alongside with him as pilot to protect Sidonia, but Kunato leaves without answering.
After that, Nagate was with Izana shocked by the sudden arrival of Ren Honoka by jumping from the top. Ren apologized for she and her sister behavior after the events that befall En Honoka. Ren also explained that Honoka sisters actually 5 years old, having undergone accelerated growth and compressed mental training. Afterwards, Ren also thank Nagate for having kept his promise to avenge Hou. From then on, Nagate and Ren is getting closer, and it makes Izana slightly disturbed.
In Captain Quarter, Ochiai report to the Captain of an escape preparations made by the Immortal Committee to leave Sidonia during battles against G542. Kobayashi let this issue because she is tired of the attitude of the Immortal Committee domineering. She also said that, if the extraction of data stored on the auxiliary brain succeed, then the existence of Immortal Committee will soon disappear.
Afterwards, Nagate goes to ERD lab to visit Placenta Shizuka again, unaware that she is not in the lab anymore.
At preview, Gauna human-form staring at Lem Star System, alone in the middle of space, calling Nagate's name with Shizuka Hoshijiro's voice.
- (When trying to save unconscious Nagate from the coalition with G542)"I won't let Nagate die. He is the light of hope for Sidonia."
- In Anime version, because using Super Hyggs Particle Cannon, the Immortal committe tried to fled from Sidonia even in the end canceled. In Manga version, they don't, there is no a scene about this.