With the rest of the Immortal Assembly dead, Kobayashi announces that Sidonia will set course for the Lem Star System, pursuing the Gauna's mothership who threatens the colonists of planet Lem VII. Meanwhile, Yure remembers about Kunato's words, when he reveals that he created Tsumugi by impregnating Placental Shizuka with human DNA, unaware that it is seemingly pregnant again. Elsewhere, Yuhata discovers that Nagate is visiting Tsumugi and meets him and Izana just when they appear to meet her again and she ends becoming friends with her as well. Sometime later, just when Tsumugi is about to sort for a joint exercise, she glimpses a large Gauna approaching Sidonia, which remained undetected by assimilating the colonists' ship and departs to attack it by herself. However, the Gauna create a massive structure to trap her and a platoon of 96 Guardian Pilots, including Nagate, depart to assist her.