Nagate and Shizuka finally back to Sidonia. Nagate heralded as hero for defeating G487 and save Shizuka, but the good news was not taken well by Norio. After returning to Sidonia, Shizuka give thanks to Nagate because saved her life and they were both ordered to undergo a medical check up.
Nagate social conditions improved, when he returned to the academy, his fellow cadet welcome him home with warm, and also give some bags of rice on his locker as an apology for the incident before. That's when Izana arrived, approached Nagate and suggested he should rest at the dorm. But Nagate want to go somewhere, where the ceremony of Akai Squad funeral. Tanikaze surprised by the Sidonia circumstances that have been returned to normal. Nagate and Izana give their respect to Akai Squad, and met with Yuhata who came to commemorate the death of her brother. Secretly, Yuhata thanks Nagate.
Once again, Kobayashi was called to the Immortal Committe Chamber. Immortal Committe response the return of Nagate with cold and cornered, but Kobayashi looking for a reason for the survival of Nagate, Immortal Committe will use Nagate as pawn to face Gauna.
Finally, Nagate back to the dorm and met with Lala Hiyama, at the same time, Shizuka appeared and they both ate together.
In Captain Quarter, Ochiai told Kobayashi that the resistance of the anti-war groups began to decrease since the return of Nagate, but there are still demonstrations that occurred.
The next day, the announcement that the members of Kunato Squad became official pilot Garde has been on display. Also simulation system has been updated with the inclusion of data from Nagate battle against G487.
In the evening, the graduation ceremony was held. With this, Norio Kunato, Shizuka Hoshijiro, En Honoka and Nagate Tanikaze has become official Garde pilot. At the party, Nagate accosted by Honoka sisters, especially Ren Honoka, she said the person who have been hit Nagate up a bloody nose was En. Not long hose, Norio came to Nagate, he apologized for the rude behavior some time ago and asked Nagate to forget about it, Shizuka mediate and Kunato Squad form quad-formation as a sign of teamwork. A moments later, Yuhata came over and formally say the gratitude for having avenge the death of Izumo Midorikawa, Yuhata's brother. Yuhata also said that now she joined the 28th geration class as pilot cadet.
Nagate approached Captain Kobayashi, to inquire about the truth of himself. The reason why Kobayashi pay attention to him more than normal and show up her secret face only to Nagate, the ability to recover from injury owned by himself, and the reason why his grandfather did not allow him to go to the surface. Captain Kobayashi just silent, and only asks for him to continue with his good work, to become the next of Knight of Sidonia.
Shizuka meet Nagate who had just finished talking with Captain Kobayashi, at the same time when where Izana and Yuhata appear. Yuhata invited Nagate to go to the "Sea" and ended with Izana and Shizuka who also tag along. However, Yuhata want to be alone with Nagate while seeing the sights of the sea, and when Izana disrupt her plan, Nagate ends together with Shizuka.
In the Kunato Resident, Norio still thinking about the problems that Nagate given to him. Norio achievement and his current position is thanks to the his hard work, but Nagate managed to transcend them easily, it makes Norio angry.
At the same time, Gauna hive-class with 20 core comes threaten Sidonia with invisible mode, Captain Kobayashi ordered Ichirō Seii to prepare an Assault Team.
Back to the sea. Nagate and Shizuka spend their time to see the sea view while talking about the origin of life on Earth from the sea. Their relationship deepened. In the middle of their conversation, they are called for another sortie.
And operation started.
Suddenly, Nagate woke up and he had been in the hospital. Nagate decided to get out of his room, and saw Honoka sisters blamed him. Izana came and surprised to see Nagate can walk with the wound he received, then took him to enter back into the room. Confusion with the current situation, Nagate decided to look at the news. Gauna hive-class yesterday defeated.
But suprisingly, Shizuka Hoshijiro was Killed In Action.