Nagate, Izana and Yuhata take a trip together to an inn and Nagate gets astonished to recognize Captain Kobayashi as the place's innkeeper. Once settled, Yuhata reveals that she obtained some info about Ochiai's secret lab and takes the others to investigate. The trio end up trapped inside the installations and take an elevator to a highly classified area where they are ambushed and sedated. Nagate awakens separated from the others and meets Yure, who reveals that the legends of Ochiai creating a Gauna/Human hybrid being are indeed true and is shown the corpse of the creature he developed using such method, from which they are manufacturing projectiles with a composition similar to the kabizashi and asks him to test the new weapon being developed from it. Meanwhile, Kunato also obtains info about Ochiai's experiments and come across a mysterious door, whose access are forbidden even to the members of his family. Nagate is sent back to the inn with Izana and Yuhata, who awaken with no memories of what happened and he feigns ignorance as well. Some time later, a colonization ship composed of pacifists who claim that if unarmed they will not be attacked by the Gauna, depart to settle on a nearby planet and Nagate is brought to Toha Heavy Industries, where both the new weapon and a new Guardian propulsion system is being developed, and reveals that the simulator they are using to make tests on both prototypes is the same one he used to train with his grandfather. When an alert of the Gauna approaching the colonization ship reaches Sidonia, Nagate offers himself to use the prototypes to reach the ship and defend it in time and Kobayashi accepts his request. Even having a hard time getting used to the new equipment, Nagate succeeds to reach the ship and destroy the Gauna before it attacks the colonists. After the mission, Nagate is called to EBD and cheers up when the Shizuka/Gauna hybrid uses a pen to write his name, before he is summoned by the Captain. On the way to br