Nagate, dem die Schuld für die Niederlage in die Schuhe geschoben wird, wird von Schuldgefühlen geplagt. Wir erfahren außerdem mehr über die frühen Jahre von Sidonia.
Nagate and the other pilots confront the three Guardian-like Gauna and during the fight, Nagate retrieves a human-like Gauna sample from one of the enemy vessels, that communicates with them through radio with Shizuka's voice leading Kunato to panic. Two of the Gauna are defeated, but the remaining one, later nicknamed "Benisuzume", retreats. After the battle, the pilots mourn five of their companions who were KIA, while Captain Kobayashi is confronted by Lala over her orders to have Nagate sortie on every mission, knowing that it may eventually lead to his death. Kobayashi then reveals that Nagate is immortal, and by not being a member of the Immortal Ship Crew that rules over Sidonia, he was seen by the other Immortals as a liability, but she claims that by having the skills of their late friend Saito, he will not die so easily. As Lala returns to the dorms, she reminisces about the events of the "Fourth Defensive War" 100 years ago when all citizens of Sidonia perished during a Gauna invasion, except for a few hundred survivors, including herself, Kobayashi and Saito, along Ochiai, who was responsabilized for such tragedy, but not killed because several important files were deleted from Sidonia's archives and relocated to an auxiliary database only acessible through his brain. After the incident, Saito disappeared without a trace, only reappearing 80 years later, aged because he had renounced his immortality. To preserve Saito's memory, Kobayashi ordered the creation of a clone of his, which was in fact Nagate, but Saito refused to have his mind transfered to the child, and kidnaps the infant Nagate with Lala's help, claiming that he will teach him his pilot skills nonetheless. Back to the present, the Gauna sample retrieved by Nagate is revealed to have the same appearance as Shizuka, and while in contaiment, it utters some words including Nagate's name.
Nagatea syytetään häviöstä, ja hän suree taistelussa kaatunutta. Sidonian varhaiset vuodet saavat valaistusta.
Tenu responsable d'une défaite, Nagate se sent coupable de la mort de ses compagnons, tandis que la lumière est faite sur le passé du Sidonia.
Mentre la responsabilità della sconfitta è imputata a Nagate, il giovane si sente in colpa per la morte di una vittima. Intanto, la storia della Sidonia viene svelata.
対惑星誘導飛翔体によって奇居子潜伏の可能性があった惑星を破壊すると、星白機を模した奇居子3体が現れる。衛人操縦士たちは3班に分かれ、それぞれ1体ずつ奇居子と戦うことになった。奇居子が星白機の回線を使い星白の声で言葉を発することに戸惑いながらも、長道たち岐神班は星白を模した胞衣をぶら下げた1体を撃破。長道はその星白を模した胞衣の回収に向かう。一方、サマリ班も対峙した奇居子を撃破するが、中園班は全滅してしまう。中園班を全滅させた奇居子は他の2体よりも明らかに強力で、操縦士全員でかかっても追い詰めることができず、仄烽も犠牲となってしまう。だが、この戦いは奇居子の突然の逃走により終了した……。ララァは長道が毎回出撃させられることを不服に思い、小林艦長を問い詰める。そこには長道の出生にも関わる重大な秘密があった。
새로운 형태의 가우나, 그것은 모리토의 형태를 하고 있었다. 그리고 그 모리토에 새겨진 식별코드는 702, 호시지로 시즈카의 것이었는데...
Los escuadrones de Samari, Nakazono y Kunato se separan y enfrentan a los Gauna 489, 490 y 491. Aunque los Gauna 491 y 489 son destruidos por los escuadrones de la Kunato y Samari, el Gauna 490 se comunica por radio con la voz de Shizuka después de matar a cada miembro de la plantilla Nakazono.
Нагатэ винят в поражении, и он испытывает чувство вины из-за потери; раскрываются ранние годы Сидонии.
