第 3 集: 奇諾比奧前往雷姆星系，而紬正面臨蓋納的隱藏威脅。
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 glimses 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. (Source: Wikipedia)
集數
- 第 1 集 · 小中和望月被寄生蟲困住，被迫控制他人，而長年則面臨失去與戰鬥。
- 第 2 集 · 戰鬥結束後，Tsumugi 揭露其 Chimera 身分，Kobayashi 則確保研究資料
- 第 3 集 · 奇諾比奧前往雷姆星系，而紬正面臨蓋納的隱藏威脅。
- 第 4 集 · 紬為西頓妮亞抵擋蓋納光束，而長良摧毀了主核心。
- 第 5 集 · Izana 和 Tsumugi 接受義肢與再生治療，Sidonia 抵達 Lem Star System
- 第 6 集 · Nagate 在 Tsumugi 附近尋找住所，同時重力光束發射器測試以意外的觸手生長告終。
- 第 7 集 · 守護者們處理武器故障，同時駕駛員們面臨新裝甲測試與個人啟示。