The episode begins in the past, shortly after the Fourth Gauna Defensive War. Professor 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, Izana got a call from her Grandma, Professor Yure. Nagate and Izana go to observe the Gauna placenta that has taken the form of Shizuka Hoshijiro. 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.
Time for break, Nagate, Izana and Numi decided to eat at the Whale's Onion. Nagate looks worried, Numi tried to comfort him by saying that placental specimens had no intention to attack Nagate. That's when, Samari Squad came to ask about the progress of research on the placenta of G451. Numi explained that the physical form is very similar to a human being and it's has reproductive organs and internal organs, also it's look like has an emotions. Ittan Samari recall the battle some time ago, where the G450 move like piloted by a human which cause her restless. But, Kōichi try to boost his ability to make Ittan fall to him by saying the more smaller gauna, more easily to defeat them and there is no one can beat him by using Hyggs particle. Ittan mock him, hyggs particle really a powerful weapon but that particle also gauna's resource of life which make them regenerate their placenta more quickly.
Meanwhile, Norio has relieved himself from piloting as the events during the previous battle had caused psychological distress. He then witnesses Captain Kobayashi, Prof Yure and Ochiai's clone entering an restricted 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 Norio was watching the events through security cameras. Norio learns more about Ochiai and 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 Planet Seven in the Lem Star System, which would move forward if 50,000 people volunteered to become colonists.
Once again, Nagate had called by ERD for another test on communication. Again, Placenta Shizuka reacts violently seemingly trying to attack Nagate, but she quickly became quiet. Nagate inquire about the state of Placenta Shizuka, and surprisingly, she responded by spelling out the Nagate's name.
During that time, an H-1 class Gauna attack Sidonia, Nagate given orders for sortie. He was shocked by Tsugumori equipped with Kabizashi and also Ichirō Seii who joined Tanikaze Squad on his premiere sortie and he told Nagate chosen as a Squad Leader.
Now, Nagate is promoted to squad leader and leads his squad on several successful battles with the Gauna, including an H-1 class G492. Nagate spends more time with Placenta Shizuka as it becomes less and less hostile as Nagate consistently communicates with it. And continuously, Nagate always get into the main article in the Sidonia news.
As time passes, both Izana and Yuhata display affection towards Nagate, but Nagate spends more time with Placenta Shizuka, which make them more worried about their relationship with Nagate in the future. They hope can spend some of his time with them.This time, Nagate is in the ERD facility, sitting in front of the container in which the placenta Shizuka maintained. He asked to Numi about the Gauna's placenta which have memory of the dead. Numi replied, from the point view of scientist, Gauna which has a human-like and memory of the dead as same as the previous human, but from the standpoint of the Sidonian, that gauna was different from the previous one.In between that, Norio having nightmares again for the umpteenth time. He was haunted by guilt over the death of Shizuka the other day.
Nagate insist that this Placenta Shizuka same as the Shizuka he know. However, his opinion was undeniable when Placenta Shizuka standing with its both feet and mimic the movements performed by Nagate. Numi reminded he again that Placenta Shizuka only placenta specimens. Nagate depressed again due to that fact.
Nagate back to his room and met with Yuhata who asked him to go on vacation with her, he agreed, and he returned to meet with Izana and also invited to take a vacation, Izana walked away before he could give an answer, and ended agree.
Numi analyses what Placenta Shizuka is staring at, as whenever Nagate is not present Placenta 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.