Now recognized as Sidonia's ace pilot, Nagate is sent by HQ to the military academy, in order to make a demonstration of his skills on the newest Garde VR simulator for the students. Meanwhile, upon passing by the door, Kunato and Mozuku discover Ochiai's abandoned lab and fall into a trap, with their bodies hijacked by parasites. Now under Ochiai's control, Kunato and Mozuku visit Numi's lab and puts her body under control of a parasite as well. When Nagate appears to visit Placental Shizuka, he learns that she was moved somewhere else. Depressed upon her disappearance, Nagate hears from Yuhata that Placental Shizuka is under custody for research and that he must not see her again. He then turns to Kunato for answers, but to no avail. Some time later, a massive Gauna approaches Sidonia and Nagate joins the sortie against it, piloting his new Garde, the "Tsugumori Kai". However, Nagate and the other pilots fail to break through the enemy's upgraded placenta until a huge Gauna-like creature appears to assist them. With Kunato acting as its pilot, the creature introduces itself as Tsumugi Shiraui.