Deep within the massive spaceship Sidonia, a hungry Nagate Tanikaze ventures outside his underground shelter, but he ends up arrested for stealing manufactured rice and admitted to the hospital for his injuries. Although managing to escape the hospital, Nagate is subdued by an arrogant Norio Kunato, before he is taken to the police station by Shizuka Hoshijiro. Instead, Ochiai escorts Nagate to see Captain Kobayashi, who proposes him to become a Garde pilot through a cadet training program for T
Eiko Yamano is killed and absorbed by Gauna 487, which soon disturbingly takes on the appearance of Eiko. Nagate regains consciousness and furiously launches a solo assault on Gauna 487 against orders, as the Heavy Mass Cannon is fired from Sidonia to drive it off. Lacking the spear-like weapon called the Kabizashi necessary to destroy Gauna 487, the surviving cadets retreat to Sidonia, while the Heavy Mass Cannon blasts Gauna 487 away. As a funeral is held for Eiko, a war with the Gauna is offi
Nagate is inquired about his fight with Gauna 487, but the Akai squad decides to leave the matter alone due to Nagate's recovery, while Yuhata is anxious to know the answers. Later that night, Nagate learns about the annual Gravity Festival taken place, in which a tournament among Garde pilots is being held. At the festival, Nagate encounters Shizuka, who pays for his teppanyaki meal. Izana feels flustered upon seeing them together, injuring herself with a candied apple when bumping into an ange
After killing the members of the Akai squad, Gauna 487 proceeds on a collision course towards Sidonia, prompting Kobayashi to order an emergency evasive maneuver by accelerating diagonally. This causes massive casualties in the spaceship's residential district, despite the efforts of the citizens to brace themselves. As Gauna 487 turns back to target the spaceship again, Nagate, Shizuka, Norio and En Honoka are ordered to salvage the Kabizashi used by the Akai squad. Just as the Kabizashi is ret
Nagate finds Shizuka, but Tsugumori runs out of power and the pair are left floating in space for seven days with limited emergency life support. Nagate details his knowledge of survival, which comes from his life underground and surpassing the high score of his grandfather Hiroki Saitō in the Type 17 Garde virtual training console when he was six years old. Meanwhile, Lala Hiyama, Nagate's dorm manager, urges a search party to be organized for Nagate, but Kobayashi refuses. The other cadets lea
Nagate and Shizuka return to Sidonia, where they are heralded as heroes for their survival of being stranded in outer space for three weeks. Nagate, Shizuka, Norio and En are promoted to official Garde pilots following their services in the battle against Gauna 487. During the festivities, Norio apologizes to Nagate for his previous behavior, as the four of them practice a clasp formation with their hands. Nagate later questions Kobayashi about why Saitō raised him underground and why his wounds
After discovering that Shizuka was among the casualties, Nagate recounts his memories during the battle against Gauna 488. Nine squads were deployed, as the Kunato squad was tasked with destroying the tail of Gauna 488 using explosives and detonating on Norio's command. However, Norio activated a private channel with Nagate and deliberately ordered him to detonate his explosives early, causing Gauna 488 to shake the other explosives loose. As the other pilots were ordered to retreat and regroup,
The Samari, Nakazono and Kunato squads split up and confront Gauna 489, 490 and 491. While Gauna 491 and 489 are destroyed by the Kunato and Samari squads, Gauna 490 communicates via radio with Shizuka's voice after killing each member of the Nakazono squad. When Hō Honoka and Ren Honoka attack Gauna 490, Hō is killed before Gauna 490 retreats, thereby aborting the mission. The surviving pilots later mourn the loss of five fallen comrades. Hiyama learns from Kobayashi that Nagate is immortal and
Shortly after the Fourth Gauna War, Yure Shinatose managed to integrate photosynthesizing with the remaining humans and restore population of Sidonia to 500,000 in the course of 100 years, roughly six generations. In the present, Nagate and Izana meet Numi Tahiro at the Extraterrestrial Research Division (ERD) to see how Placental Shizuka would react in Nagate's presence, but she instead reacts violently while in containment. Meanwhile, Norio, who no longer can pilot due to psychological distres
Nagate, Izana and Yuhata travel to an inn, where Kobayashi is shown as the innkeeper. After Yuhata shares written proof about Ochiai's forbidden research to Nagate and Izana, the three go to an old research facility to investigate. However, they are soon sedated by security guards after they take an elevator. After being awaken by Yure and Kobayashi, Nagate is shown a Gauna/human hybrid corpse, and explained how artificial Kabi can be manufactured to destroy the Gauna. Kobayashi then appoints Na
Gauna 542 is detected approaching Sidonia, as it is revealed to be a massive pod shown as 8,000 times the size of Sidonia which its placenta has covered an asteroid. Even when Yuhata maneuvers Sidonia with its thrusters, Gauna 542 changes its path to maintain a collision course. Kobayashi orders that all 48 Garde pilots be equipped with the SHS-BAD and be deployed, while an Interplanetary Missile is launched at Gauna 542, two hours before impact. As the pilots evenly divide into two platoons, th
After the Heigus Particle Cannon makes impact, the 14 Garde pilots regroup and attempt to break into the placenta. With her Garde damaged, Ren entrusts Nagate with her last core-piercing projectile before she withdraws from battle. Nagate confronts the Crimson Hawk Moth in a vicious duel, even with daring help from Izana, while Ittan Samari and the seven remaining pilots make their way to destroy the host core of Gauna 542. Kōichi Tsuruuchi exhausts his power supply to break through the last bar