Nagate and Shizuka return to Sidonia where they are heralded as heroes and for their services in the last battle, Nagate, Shizuka, Kunato and En Honoka are promoted to official Guardian pilots. In the occasion, Kunato apologizes to Nagate for his previous behavior towards him and Nagate meets Captain Kobayashi, with questions for her about why his grandfather raised him in the underground and why his wounds heal an accelerated rate, but the Captain only asks for him to continue with his good work. After the party, Nagate is approached by Yuhata who asks him to accompany her in a underwater ride and Shizuka and Izana accompany them. However, Yuhata attempts to get alone with Nagate in a bathysphere and when the others interfere, Nagate ends up riding alone with Shizuka instead. The two spend some quality time until they are called for another sortie, as a large Gauna pod is seen approaching Sidonia. Nagate departs to confront the Gauna 488 with Shizuka and wakes up some time later in the hospital, where he learns, to his horror, that Shizuka was killed in the battle.