Nagate und seine Crew schließen ihr Pilotentraining ab und werden bei Rückkehr des Feindes sofort in die Schlacht entsandt. Kunato nimmt sich Nagates Vergangenheit vor.
Nagate and Shizuka return to Sidonia where they are heralded as heroes and for their services in the last battle, Nagate, Shizuka, Kunato and En Honoka are promoted to official Guardian pilots. In the occasion, Kunato apologizes to Nagate for his prevoius behavior towards him and Nagate meets Captain Kobayashi, with questions for her about why his grandfather raised him in the underground and why his wounds heal an accelerated rate, but the Captain only asks for him to continue with his good work. After the party, Nagate is approached by Yuhata who asks him to accompany her in a underwater ride and Shizuka and Izana accompany them. However, Yuhata attempts to get alone with Nagate in a batysphere and when the others interfere, Nagate ends up riding alone with Shizuka instead. The two spend some quality time until they are called for another sortie, as a large Gauna is seen approaching Sidonia. Nagate departs to confront the Gauna with Shizuka and wakes up some time later in the hospital, where he learns, much to his horror, that Shizuka was killed in the battle.
Nagate ja hänen ryhmänsä valmistuvat piloteiksi ja saavat tuota pikaa käskyn liittyä taisteluun. Kunato tutustuu Nagaten taustoihin.
Nagate et ses amis décrochent leur diplôme de pilote et sont rapidement envoyés au combat à l'approche de l'ennemi, pendant que Kunato s'intéresse à l'histoire de Nagate.
Terminato l'addestramento, Nagate e i compagni vengono mandati in battaglia contro il nemico. Intanto, Kunato indaga sulla storia del giovane.
256機の衛人によって救出された長道と星白。シドニアへ戻ると、長道は英雄的な扱いを受けるまでに至り、岐神、星白、仄焔とともに正規操縦士に任命される。先の戦いでの活躍が大きく評価されたのだ。任命式では岐神と和解。4人は新たな仲間として掌位を組むのだった。一方、長道は自身の境遇に疑問を持ち始め、小林艦長に疑問をぶつけるが、艦長は「シドニアの騎士になってくれ」とだけ伝え、就任式の場から去っていくのだった。艦長のもとを去った長道は星白と海中浮遊槽を楽しみ、お互いの距離を縮めていくのだが……。シドニアの航路に新たな奇居子が出現し、出撃を余儀なくされてしまう。
수비대에 의해 목숨을 건진 타니카제와 호시지로는 가우나 격퇴의 공을 높이 사 함께 출격했던 쿠나토, 엔과 함께 정규 조종사로 승격된다. 그리고 표류 사고로 사이가 깊어진 두 사람은 꿈과도 같은 시간을 보내게 되는데...
Nagate y Shizuka vuelven a Sidonia, donde son recibidos como héroes por su tenacidad de aguantar tanto tiempo a la deriva en el espacio exterior. Nagate, Shizuka, Norio y En son ascendidos a pilotos oficiales de Garde tras su servicio en la batalla contra el Gauna 487.
