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 to 500,000 in the course of 100 years (six generations). 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 Extraterrestrial Research Division (ERD), who wants to use Nagate in a series of tests to see how Placenta Shizuka would react in his presence. Nagate tries to communicate with her 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 entering an unknown area. The Captain retrieves terraforming knowledge 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. Kunato learns more about Ochiai and is interested of the "great power" Ochiai attempted to obtain. As anti-war protests continue to increase Kobayashi intends to remove them from Sidonia by allowing them to colonize and terraform the 7th planet in the Lem star system, which would move forward if 50,000 people volunteered to become colonists. As time passes both Izana and Yuhata display affection towards Nagate, but Nagate spends more time with Placenta Shizuka 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, including an H-1 class Guana 492. After many battles Nagate agrees to go on a vacation with Izana to take a break. Numi analyses what Placenta Shizuka is staring at, as whenever Nagate is not present ena Shizuka would constantly stare at one point in a wall within its confined space. It is then revealed that Placenta Shizuka 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 kabizashi storage site.