Ep. 12: Nagate confronts Benisuzume while Samari's platoon infiltrates the Gauna pod to destroy the Master Gauna.

After the Heigus beam impact, damaged pilots regroup to breach the enemy placenta. Ren Honoka gives Nagate her final core-piercing projectile to defeat Benisuzume and avenge Hou, then withdraws with unit 314. Nagate duels Benisuzume, losing consciousness until Izana saves him but gets injured herself. Nagate fires Tsugumori's left hand containing Ren's projectile to destroy Benisuzume. Meanwhile, Samari's platoon enters the Gauna pod. Pilot Kōichi Tsuruuchi uses his last Heigus to break the final barrier, allowing the group to destroy the Master Gauna's core. Samari, Seii, and Tsuruuchi escape as an anti-planetary missile destroys the target. On Sidonia, Ren thanks Nagate for avenging Hou and reveals she and her sisters are only five years old due to accelerated growth. Nagate visits Kunato, who plans to quit; Nagate expresses a desire to fight alongside him despite unresolved feelings, but Kunato departs without reply. Nagate then seeks Placenta Shizuka, unaware she has left the lab.
Episodes
- Ep. 8 · Nakazono, Samari, and Kunato squads battle Gauna while Nagate retrieves a sample resembling Shizuka.
- Ep. 9 · Nagate bonds with Placenta Shizuka while Kunato uncovers secrets about Ochiai and terraforming plans.
- Ep. 10 · Nagate investigates forbidden research and pilots untested weapons against a massive Gauna threat.
- Ep. 11 · Sidonia faces Gauna pod 542 while pilots deploy 48 guardian frames in a desperate collision avoidance strategy.
- Ep. 12 · Nagate confronts Benisuzume while Samari's platoon infiltrates the Gauna pod to destroy the Master Gauna.