The episode begins with a recap of the ending of the previous; Nagate in the Tsugumori is stricken down and heavily injured, while team leader Eiko Yamano's Garde is speared and disabled, by a surprise attack from a gauna which hidden in the comet they were sent to mine for ice.
The episode cuts back to before the mission, Izana introduces Nagate to a superstitious ritual in which pilots who are going to fly together for the first time mimic the clasp-formation they perform together in their Gardes in flight, lest they befall ill fortune. Izana invites Yamano to join them, though she refuses, scorning the superstitious is stupid. As she walks away, she frustratedly reflects on the unfairness in being grouped together with "special cases", she feels somewhat resentful that despite having been around for such a short amount of time, Nagate is already her equal, whereas she, a girl from a sparsely-populated section of Sidonia, had to struggle and work hard to get to where she was now.
As memories of her friends, family, and neighbors congratulating her on her becoming the first pilot from their community flood her mind, the gauna begins to crack open the cockpit of her Garde, snapping her back to reality. Screaming in terror, she pulled from her now-shattered Garde by the gauna's tentacles towards its gaping maw. As she cries out in despair, the gauna's tentacles toss her into its mouth, damaging her suit's computer in process and thus preventing her from using it's propulsion jets to try to escape. Moments after the gauna's "mouth" closes around her, her cries over the comms are abruptly silenced, briefly replaced by an horrific gurgling digesting sound, and then permanent silence. The other cadets, whom have yet to finish their training, are frozen in shock and fear, unable to do anything to help their now-devoured comrade.
The gauna immediately launches an attack against the other cadets, lashing out with its tentacles and knocking one of the Honoka sisters' Garde off its feet. Before it can finish her off, her sister rushes in, cuts the gauna's tentacles, and pulls her to safety. Kunato briefly considers attacking the gauna, but when the gauna attacks him, he retreats as well. As Izana fights to fend off the gauna's attacks, she can only look on in terrified as the gauna prepares to finish off the stricken Tsugumori. However, before the gauna can do it, Nagate, who was in a state of cardiopulmonary arrest (in other words, his heart had stopped) with a broken spine, suddenly revive, and at the last moment he cuts the tentacle away with the T-17's high-vibration blades, much to the surprise of everyone both in the field and back at Sidonia's command center.
At the same time, Captain Kobayashi has ordered Sidonia to open fire on the gauna with her Heavy Mass Cannon. No one of cadets garde equipped by Kabizashi, the only weapon known to be capable of killing the gauna, and because of that, the only available option is to knock the gauna away. As Executive Officer, Ichirō Seii commands the cadets to retreat, Nagate furiously engages the gauna, which begins mimicking Eiko's form. Ignore the pain of his injuries, Nagate unleashes a barrage of fire from the Tsugumori's gatling cannons, along with firing a pair of missiles into "Eiko's" face and blowing it apart, dodging the gauna's attacks and buying the other cadets time to retreat. Unable to effectively move the Tsugumori's legs due to his injuries, he is tripped by a leg-sweep from the gauna's tentacle, only to be saved by Shizuka Hoshijiro grabbing him and pulling him away and then by Kunato launching a barrage of missiles at the tentacles as they try to pursue the two. The seven surviving cadets enter into Clasp Formation and boost away, just as the HMC's enormous shell impacts into the comet and the gauna, destroying its placenta and sending its stunned and "unconscious" core tumbling away from Sidonia.Command and center staff can breathe a sigh of relief for now, but Kobayashi reminds them not to get their hopes up; they've only merely knocked the gauna back, and it will return before long. She departs to the Immortal Council Chamber for debriefing and discusses the Large Mass Union Ship which is three light-years out from Sidonia. Meanwhile, despite the gauna's re-emergence, anti-war demonstrator are seen decrying the claims and stating that Eiko's death and the gauna's re-appearance is a lie fabricated by the military to provide an ongoing excuse for the Immortal Ship Council, who are in fact merely rumored to be a conspiracy theory, to remain in power.
A funeral is held for Eiko Yamano, and at the same time Kobayashi announces the return of the gauna and the resumption of war against the enigmatic aliens. Afterwards, it is shown that many of the more superstitious cadets have begun to believe Tanikaze (who has already somehow fully-healed despite the grievous nature of his injuries) is cursed; in their eyes, it seems more than a mere coincidence that as soon as he appears and becomes a pilot, the gauna attack. To make things become further complicate, information about the attack is withheld from anyone who are not official pilots or, obviously, weren't present during the incident. Other cadets ask Nagate and Izana about the attack, but remembering their orders, they hastily excuse themselves to avoid answering the questions.
Later, the cadets' classes resume, during which time it is revealed why and how humans on Sidonia can photosynthesize: Roughly a century ago, Sidonia's food production were destroyed during an attack by the gauna, and in order to make up for this, the next generation of Sidonia's children are genetically-engineered to be capable of utilizing high-concentration photosynthesis to drastically cut down on their food-consumption needs, resulting in virtually all Sidonians needing to only eat once a week. During the lesson, a couple cadets snidely reference Nagate's inability to photosynthesize, the implication being that their comments are derogatory. Why this is the case is not entirely clear, although the term "photosynthesizing" is used both in reference to the obvious, and in sexual connotations, so perhaps the insult is that he's incapable of sexual interaction. In either event, Izana snaps at the offending group to be quiet, while Nagate numbly and blankly sits without responding to anything.
The mocking from his classmates continues; when Nagate opens his locker after class, he finds a large bag of deodorizing powder inside. Some of the nearby students jeer at him that he smells and that he needs to stop eating too much. Ichirō Seii, who walks into view immediately after this, notices Nagate is not wearing his gravity belt, a basic safety implement used to secure crew against gravity malfunction. Realizing he has never been instructed on the gravity belts, Ichirō tasks Nagate with testing the securing bars around the academy. During this time, Nagate unwittingly stumbles into the girl's locker room. He is subsequently decked by the martial-arts-trained Honoka sister, En, and knocked out.In the place of Tsugumori displayed before, some cadets talked about the Nagate and his machine state, and a green-haired woman interested in these rumors. She began investigating on Nagate, watch the list of his machine repair record and was amazed by his ability.Izana approached Nagate and asked him to go to grave of Eiko Yamano with her, but Nagate end up fainted when he saw Eiko's name carved in black gravestone. Nagate always haunted by the nightmare that causes him to have difficulty sleeping and always nausea. Izana feel sorry for him.
The conversation continues, Izana tells of the events a hundred years ago, when Sidonia attacked by two Gauna and nearly destroyed, and also stories of heroism of Tsugumori. Izana then ask Nagate about his pilot skills using Tsugumori. Nagate replied that he often practiced with Type 17 VR Simulation at underground. Izana also said, Garde Type 17 and Tsugumori made by Toha Heavy Industry, while the currently main unit, Type 18 made by Kunato Development, so the design and the system is quite different. Izana argues, Tsugumori suitable for Nagate.
The previlous Gauna, G487, intends to threaten Sidonia once again in about 3 days. Ichirō Seii, as Executive Officer, formed Assault Team consisting of four veteran pilot, Mochikuni Akai, Kashiwade Aoki, Izumo Midorikawa, and Hinata Momose.
Tanikaze come to cafetaria to eat, and he met Lala. Even though it has only been three days, his bones have healed, but he is forced to remain wearing the casts. When viewing the news coverage on television, Nagate are reminded to previous battles and fade out. Lala took him to the academy's pharmaceutical. Nagate woke up and found himself treated by Captain Kobayashi, but she was denied that she is the Captain. Nagate recall a few days ago when he met Captain Kobayashi for the first time, and he vowed to become a pilot who will protects Sidonia.
Assisted by Shizuka Hoshijiro, Nagate back to class. Nagate apologized to her because he has been troublesome and the other things. But Shizuka ignore it and say that he did not stink of vomit or troubling her. At the end of the conversation, Nagate's stomach rumbling and Shizuka laughed merrily.
After school, member of Akai Squad, pay a visit to the academy. Meanwhile, green haired girl came to academy to search Nagate. And Izana, who was looking for Nagate too, gets flustered upon seeing Nagate and Shizuka together. Word about Akai Squad came to academy gets out to the cadets, and Kunato with his friends assume they are there to see him, but are shocked when Akai completely ignores them. Instead, Akai approaches Nagate, make Kunato furious. Finally, green haired girl met with Nagate and introduce herself as Yuhata Midorikawa.