Die Gauna versuchen, die Angriffstruppen auf beunruhigende Weise zu entmutigen und zu besiegen, doch Nagate kehrt mit einem vielversprechenden Preis nach Sidonia zurück.
The episode begins in the past, shortly after the fourth defensive war. Doctor Yure manages to integrate photosynthesizing with the remaining humans and restores Sidonia's population. In the present Nagate and Izana go to observe the Gauna placenta that has taken the form of Shizuka. They both meet Numi Tahiro, a scientist at EBD, who wants to use Nagate in a series of tests to see how the Shizuka/Gauna hybrid would react in his presence. Nagate tries to communicate with the Gauna by mentioning Shizuka's name but it reacts violently seemingly trying to attack Nagate. Meanwhile, Kunato has relieved himself from piloting as the events during the previous battle had caused psychological distress. He then witnesses Captain Kobayashi, Dr Yure and Ochiai's clone enter an unknown area. The Captain removes unknown details from a site known as the auxiliary brain using the Ochiai clone, as only Ochiai's mind can enter the database, the clone is then put to sleep by the Captain's orders but she is unaware that Kunato was watching the events through security cameras. As time passes both Izana and Yuhata display affection towards Nagate, but Nagate spends more time with the Shizuka/Gauna hybrid as it becomes less and less hostile as Nagate consistently communicates with it. Nagate is also promoted to squad leader and leads his squad on several successful battles with the Gauna, after many battles Nagate agrees to go on a vacation with Izana to take a break. Numi Tahiro analyses what the Shizuka/Gauna hybrid is staring at, as whenever Nagate is not present the hybrid would constantly stare at one point in a wall within its confined space. It is then revealed that the hybrid is actually staring at where the kabizashis are stored, far off in another part of Sidonia, seemingly scared. In the distance Benisuzume stares intently at Sidonia and at the kabizashis storage sight.
Gaunat löytävät huolestuttavan keinon vastustajan löylyttämiseen. Nagate palaa Sidoniaan, mukanaan jotakin mistä voi olla apua.
Alors que les Gaunas ont trouvé un moyen inquiétant de contre-attaquer leurs adversaires, Nagate est de retour sur le Sidonia.
I Gauna trovano una modalità dolorosa per sconfiggere la forza d'attacco, mentre Nagato rientra sulla Sidonia con qualcosa che potrebbe tornare utile in battaglia.
エナ星白を保存する外宇宙生命体研究所、通称「外生研」。長道の名前をつぶやいたエナ星白の知性を確認するため、研究者・田寛ヌミが実験を行う。
実験は長道が実験槽の前に立ち、エナ星白の反応を窺うというもの。エナ星白は長道に向けて胞手を伸ばし、実験槽を叩くという反応を見せた。
一方、小林艦長たちはある儀式のため、岐神家を訪れていた。儀式について知ることは、岐神家でも当主にしか許されていないというのだが……。
외 우주생명체 연구소 요청으로 연구소에 도착한 나가테는 호시지로를 모방한 에나 와 만나게 된다. 그 에나는 나가테를 보자마자 다른 반응을 보이기 시작했는데...
Poco después de la cuarta guerra Gauna, Yure Shinatose logró integrar la fotosíntesis con los supervivientes de Sidonia y restaurar su población a 500.000 habitantes en el transcurso de 100 años. En la actualidad, Nagate recibe una invitación para visitar un complejo secreto de investigación.
Гауна находят ужасающий способ деморализовать и перебить атакующие войска. Нагатэ возвращается в Сидонию с трофеем, который может помочь в этом сражении.