The massive Gauna identified as G542 detected by Sidonia's radar, the size of the 8000 times larger than Sidonia, with 200 core, and its placenta covered a dwarf planet, moved toward Sidonia at high speed. Unknown, G542 intend to conduct collisions with Sidonia. Responding to this situation, Executive Officer Yuhata proposed that Sidonia to perform an evasive maneuver and avoid collision with the G542.
At that time, in the ERD lab, Numi receive an incoming call from Prof. Yure asking how the Placenta Shizuka reaction when G542 approaching Sidonia. Numi replied, Placenta Shizuka still continue to pay attention to Kabizashi in the storage room. Numi ask again why Gauna attack Sidonia again when G451 attack the colonists ships. Prof Yure answer, there is no doubt Gauna has a special affinity with Kabi, but despite throwing Kabizashi, Sidonia still be threatened by Gauna.
After preparation of evasive maneuvers, Sidonia began to move to avoid a collision. However, the G542 turn directions and create a new collision course with Sidonia. Not only that, the G542 also change it's placenta resembles the propulsion system that caused it can move fast, it can still crashing with Sidonia although she uses the highest speed. And in the next 6 hours, Sidonia will collide with the G542.
Executive Officer Yuhata decided to shoot G542 with Anti-Planetary Missile. But based on the record of the previous battle, Gauna can avoid the missiles fired towards it and also can destroy it with Hyggs Particle Cannon. To deal with that problem, Sidonia will send Gardes Assault Team to attack Gauna that blanketing the dwarf planet.
Anti-Planetary Missile fired from Sidonia to G542. 48 units Gardes equipped with SHS-BAD and also CPP, launched from Sidonia incorporated as Gardes Assault Team in 2 Platoon. With frame formation, Gardes Assault Team moves into operation. Yuhata as Executife Officer explained the course of the operation, Gardes Assault Team will destroy all Gauna that surrounds the dwarf planet before the missile hit the target.
Nagate then had a flashback a moment ago, when he came to the Captain Quarter. Captain Kobayashi told him about a hero in the past that continues to save Sidonia from threat of Gauna, who turns out he was Hiroki, and Kobayashi said that Sidonia currently need a new hero, namely Nagate Tanikaze. Nagate said that he didn't deserve to be aligned with the hero of Sidonia in the past, but he was willing to protect Sidonia and he accepts the fact that he is the Knight of Sidonia.
Gardes Assault Team has passed the Anti-Planetary Missile and soon to carry out operations in the area. The pilot began to fret with this operation will become a very difficult mission, Ren and Ittan tried to calm them.
Back to Sidonia, in Kunato residence, there Norio was remembering his past, about Nagate who has taken his role as pilot of Tsugumori. He then murmured about his opinion regarding the supposed Tsugumori piloted by himself.
All pilots were surprised by the size of the G542. The operation then begins. 1st Platoon commanded by Ittan Samari, tasked to look for and battle against the cores of Gauna. Platoon 2 tasked to destroy the propulsion system and stop its movement before crashing to Sidonia.
1st Platoon began their attack to the G542, several core is exposed fired and immediately decomposed into bubbles. Some pilots are have some difficult because not accustomed to aim and shoot, but Nagate calmly pulled the trigger and shot one by one Gauna's core with one shot.
While 2nd Platoon to move to the back, to the G542 propulsion system that drives the dwarf planet. Gardes shot with Hyggs particle cannon and CPP to destroy it.
But then, the Gauna's core faced by 1st Platoon start changing it's placenta to make Hyggs particle emitter. Gauna firing particle beam to counter attack the garde, unit 278 is the first shot down. Because Gauna began to return fire, 1st Platoon decided to go to surface of the dwarf planet, so they can easily fired on target. Long barrel mounted on SHS-BAD discarded because they would strike the long barrel with G542 in close range and also to make the movement of Gardes more easily controlled. There is a system error that makes long barrel can not be removed, so that some units Gardes crashed because the machine is difficult to control.
On the other hand, 2nd Platoon operations fairly easily, it is because not too many Hyggs particle emitter there. After take some hit, the propulsion system G542 receives the impact of the attack. However, it was not for so long, when a sudden attack hit the 2nd Platoon Commander and make his Garde explode. Quickly, one by one member of the 2nd Platoon defeated, when only one Gauna that they face.
One reason for the annihilation of 2nd Platoon is due a loss of co-ordination with each other since their commander shot down. One other reason is because they are attacked by Benisuzume, the most dangerous and powerfull single core Gauna. In a few minutes, 2nd Platoon was annihilated.
Meanwhile, 1st Platoon began to find their momentum, since they attack from close range. But the problem occures, CPP ammunition of 1st Platoon is running out and only the remaining 14 units which can operate.
Sidonia circumstances worsen, Yuhata quickly formulates a new plan: to activate Sidonia's Super Hyggs Particle Cannon and fire it at the head of the Gauna. This would then allow the remaining pilots of 1st Platoon to fly into the Gauna structure to locate and destroy the 'Mother Core', which supposedly controls the massive Gauna. However, firing Sidonia's cannon will require rerouting her entire power supply and will temporarily consume all her Hyggs particles, leaving Sidonia without propulsion to maneuver away from collision course if the plan fails. With no other option, the Captain approves the plan and the Sidonia fires the Super Hyggs Particle Cannon at the G542.
- In the Anime version, the pilot who participate in this operation is 48 units. In the Manga version, however, 96 units.
- In the Anime version, the dwarf planet completely warped by the placenta of G542. In the Manga version, Gauna placenta only focused in propulsion system and the asteroid can be seen by naked eyes.
- In the Anime version, Sidonia fire her Super Hyggs Particle Cannon to eroded G542 placenta in order to destroy the Mother Core. In the Manga version, Sidonia didn't fire anything because there are no placenta covered the dwarf planet.