Der Pilot Nagate Tanikaze ist nun für seinen Erfolg im letzten Kampf bekannt, jedoch macht er sich Sorgen über Shizuka Hoshijiros Verschwinden.
Kunato and Mozuki discover Ochiai's abandoned lab and fall into a trap resulting in their bodies hijacked by parasites. Now under Ochiai's control, Kunato and Mozuki visit Numi's lab and put her body under control of a parasite as well. When Nagate visits the Placental Shizuka, he learns that she was moved to a new location for research and that he can not see her again. He then turns to Kunato for answers, but to no avail. Meanwhile a massive Mauna approaches Sidonia and Nagate joins the sortie against it, piloting his new guardian, the "Tsugumori Kai". However the attack fails to break through the enemy's upgraded placenta. But then another Gauna-like creature appears, and with a single shot it causes massive damage to the giant Gauna. The new mysteriuos Gauna introduces itself as Tsumugi Shiraui.
Le pilote Nagate Tanikaze est désormais célèbre pour ses récents faits d'armes, mais Nagate est plus préoccupé par la disparition de l'ena d'Hoshijiro.
Il successo per le imprese in battaglia non distrae Nagate Tanikaze dalla preoccupazione per la scomparsa di Ena Hoshijiro.
太陽系を滅ぼした謎の生命体・奇居子（ガウナ）と交戦しながら新天地を目指す潘種船シドニア。めざましい戦果を挙げる衛人（モリト）操縦士・谷風長道（たにかぜながて）は、操縦士訓練の憧れとなっていった。しかし、本人が気にしているのは外生研から消えたエナ星白の行方ばかり。
시도니아의 룰을 어기고 금기구역이었던 오치아이의 연구실에 발을 들인 노리오. 그것은 시도니아의 새로운 위기를 초래하는 전조였는데...
Ahora reconocido como el piloto as de Sidonia, Nagate Tanikaze es enviado a la sede de la academia militar, con el fin de hacer una demostración de sus habilidades en la nueva consola de formación virtual Garde a los estudiantes.
