Plot EditNagate, Izana and Yuhata take vacation together, but actually Izana or Yuhata want to go alone with Nagate.
This time the destination is a little-known inn, which surprised Nagate was Captain Kobayashi impersonate the owner of the residence. This inn is located on the surface of the reservoir of Sidonia. When resting, Yuhata issued a book containing diverse urban legend on Sidonia, such as the truth of Immortal Committe. In the book also says, about an experiment conducted by an genius scientists named Ochiai involving about Gauna / Human Hybrid. Actually, there is another reason why Yuhata chose this place as a vacation spot, she wanted to make sure the truth about this.
At the time, in the ERD lab, Yumi noticed that the Placenta Shizuka has a special interest in Kabizashi, stored in the container, or when used by Garde in battle. Yumi warned it to Prof. Yure and she was warned to be careful and keep an eye on it.
Nagate with his friend to go to a place that believed to be a former facility of Ochiai, using the keys found by Yuhata, they entered into the facility. There, Izana started to panic and beat Nagate involuntarily. Stuck without a way out, Nagate with his friend decided to go exploring this place. Nagate found and fix broken elevators and hence Izana suddenly remembered the nickname of Nagate, "The Mole Man". They arive at a place in zero gravity area, and found the entrance to the MSCF 5, a high-security isolation ward. There, they met with a member of the Immortal Committe, surrounded and sedated by security.
Nagate woke up and found himself with Yure, who was the grandmother of Izana and a member of Immortal Committe, but Yure ask Nagate to conceal her true identity from Izana. Then he showed a Gauna / Human hybrid, a Chimera, who reveals that the legends of Ochiai creating a Gauna/Human hybrid being are indeed true. Yure continues to explain that both the Gauna-Human hybrid and the Kabizashi emit a radiation which attracts the Gauna to the Sidonia, and then Captain Kobayashi appears, continuing the explanation about this Chimera. The corpse of the hybrid, which scientists have been able to use to manufacture artificial kabi with which to destroy Gauna, thus reducing reliance on the limited number of Kabizahi. Also, the new weapon system curently manufactured by Toha Heavy Industries. Captain Kobayashi says, that Nagate will be the test pilot for the new weapons system.
Meanwhile, Norio also reads about Ochiai's experiments and comes across a mysterious door, access to the which is forbidden even to the members of his family.
In ERD lab, Placenta Shizuka experiencing growth in communication, now its can write the name of Nagate.
Some time later, a colonization ship carrying settlers, who claim that the Gauna only attack because of the Kabizashi and will not attack unarmed humans, departs to settle on a nearby planet, to Planet Seven in Lem Star System. At night, Izana dreams she can also live on a planet with peace.
After that, Nagate is brought to Toha Heavy Industries, where both the new weapon, Super High Speed Ballistic Acceleration Device (SHS-BAD), a long-range projectile launcher, and a new Guardian propulsion system are being developed. It is revealed that the both technologies and the simulator which they develope to make tests on both prototypes is the same one Nagate used to train with his grandfather.
When the Sidonia discovers G541 moving to intercept the colonization ship, Nagate offers to use the prototypes to go after the Gauna and defend the ship, a supposedly impossible feat as the equipment does not have automatic stabilization and is completely untested. However, Nagate states that he has used it in his grandfather's old simulator, and Kobayashi approves his request to launch.
In waiting room, the other co-pilot saw an explanation of the SHS-BAD and Gauna Core Piercing Projectile or CPP, and watch Nagate on mission.
Nagate begin the mission to engages G541. Despite missing his first shot at 230 km range and losing control of his frame from the massive recoil. Nagate successfully re-stabilizes and destroys the Gauna with a second shot in 210 km, moments before Gauna reaches the colonization ship. Make CPP proved able to decomposes the Gauna. Now, Sidonia Garde pilot can enganges Gauna in distance.
After the mission, Nagate is called to the ERD because there is Placenta Shizuka want to show him, an new "apperance" and when Placenta Shizuka uses a pen to write Nagate name. Nagate very pleased with the development of the placenta specimens of G451, but after that he is summoned by the Captain.
En route to the briefing, Nagate meets Izana, who tells him that she has just been promoted as a pilot, and, knowing the low survival rates, especially among new pilots, is distressed as she believes her time with Nagate is soon to end. Nagate attempts to reason with Izana, who, upset upon guessing that he was visiting Placenta Shizuka again, runs away, nearly falling to her death after slipping, although he saves her just in time.
Meanwhile, at the Command and Center Room, a massive Gauna pod, 8.000 times the size of the Sidonia, is detected rapidly approaching the ship.