Während sich Nagate zur Bezwingung einer alten Bedrohung zum Piloten ausbilden lässt, muss er sich an das Leben in der jahrhundertalten Weltraumsiedlung gewöhnen
At the massive spaceship Sidonia, having exhausted his last supplies of food, Nagate Tanikaze ventures outside home to look for food when he is spotted and captured by the local security while trying to steal some rice. Believing that his life is at risk, Nagate manages to escape the hospital where he is being treated just to be apprehended by some military cadets. One of the cadets, Shizuka Hoshijiro, accompanies Nagate while he is being questioned by the police, when a man called Ochiai appears and takes him to Captain Kobayashi, the highest authority of Sidonia, who claims that she intends to take him under her guard, with the condition of becoming one of Sidonia's Guardian pilots, to which he accepts. He is then registered as an official cadet and introduced to the others. In the occasion, Nagate learns that the Guardian pilots' main mission is to defend Sidonia against an alien hostile species known as the "Gauna", although the last time they encountered them was a hundred years before, and befriends Izana Shinatose, an hermaphrodite whose body can be adapted to procreate with either males or females, depending of the chosen partner. After failing to impress his peers at the pilot simulator, as the controls are different from those he trained to perfection at his former home, Nagate is called to his first sortie along Shizuka and Izana, but instead of piloting one of the recent Type 18 models, Nagate is entrusted with Tsugumori, a legendary Type 17 unit that belonged to a famous war hero, much to the anger of Norio Kunato, a cadet who always wanted to become its pilot and is being dispatched with him as well. Realizing that Tsugumori's controls are similar to those he is used to, Nagate's confidence is renewed but while performing a mining operation at a nearby asteroid with the others, a Gauna appears from inside it and attacks them.
Nagate on elänyt eristyksissä koko elämänsä. Nyt hänen on totuteltava elämään ja koulutukseen ikivanhassa avaruusyhdyskunnassa
Né dans une colonie de l'espace fondée il y a plusieurs siècles, Nagate fait ses armes en tant que pilote pour combattre un vieil ennemi.
Cresciuto in isolamento, Nagate deve abituarsi a vivere su una nave colonia centenaria, mentre è addestrato come pilota cadetto per fronteggiare un'antica minaccia.
謎の異生物・奇居子（ガウナ）によって太陽系を破壊され、わずかに生き残った人類は巨大な恒星間宇宙船シドニアでの旅を余儀なくされた。その出航から、約1000年――。
シドニアの地下で祖父にひっそりと育てられた谷風長道（たにかぜ ながて）は、祖父の死後、食料が尽きたことで地上へ出ると、米泥棒の容疑で逮捕されてしまう。窮地を救ってくれたのはシドニアの艦長だった。彼女に保護され、人型巨大装甲・衛人（モリト）の操縦士訓練学校に入学することになった長道は、初めて見る祖父以外の人間たちと交流を深めていく。そして、かつての英雄が乗っていたという一七式衛人（モリト）白月改・継衛（ツグモリ）を与えられ、初任務に就くのだが……。100年ぶりに姿を現した奇居子に遭遇してしまう。
태어나서부터 줄곧 지하층부에서 살아온 소년 타니카제 나가테. 할아버지의 죽음이후 떨어진 식량을 찾기 위해 길을 나섰던 그는 지금까지 보지 못했던 새로운 세계와 만나게 되는데...
En lo profundo de la enorme nave espacial de Sidonia, Nagate Tanikaze un chico que vive en las profundidades de la nave al margen de la sociedad que la habita, se aventura fuera de su refugio subterráneo en busca de comida, cuando es descubierto y atrapado por las fuerzas de seguridad de Sidonia al tratar de robar un saco de arroz.
Нагатэ, всю жизнь проживший в изоляции, вынужден приспосабливаться к жизни в многовековой космической колонии, одновременно обучаясь на пилота-кадета для борьбы с древней угрозой.
