Set in the year 3394, humanity survives inside the Sidonia, a massive, seed-like generation spaceship fleeing the remnants of the solar system after mysterious, shape-shifting alien monsters known as the Gauna destroyed Earth. Nagate Tanikaze, a young man raised in the deep, forgotten subterranean levels of the ship by his grandfather, struggles for survival after his grandfather's death. Forced to the surface to steal food, Nagate is arrested but quickly recognized for his unique background and inherited piloting skills. He is drafted into the elite corps of Guardian pilots, the mecha defenders tasked with protecting the Sidonia from looming Gauna threats.Nagate is assigned to pilot the ancient Type-17 Guardian, a legendary mech that matches his grandfather’s combat style. Despite facing prejudice from his peers due to his underground origins, Nagate quickly proves his mettle in battle against terrifying Gauna forms. He is joined by diverse comrades, including Shizuka Hoshijiro, a talented pilot with whom he shares a deep, tragic bond; Izana Shinatose, a member of the Sidonia’s neuter third gender; and Yuhata Midorikawa. Nagate’s unorthodox tactics and innate talent earn him the respect of his commander, Captain Kobayashi, who holds dark secrets about the true nature of the Sidonia, the immortal Council, and the looming war.As the series progresses, the Sidonia faces increasingly perilous encounters, including a massive Gauna assault that forces the ship into desperate tactical maneuvers. Nagate’s mech is upgraded with advanced alien-human hybrid technology, allowing him to wield the coveted Kabizashi—the only weapon capable of destroying a Gauna's immortal core. Alongside this combat, a deeper conspiracy unfolds regarding the ruling elite's manipulation of human genetics, photosynthesis adaptations, and the creation of hybrid soldiers designed to win the war at any cost.Tragedy strikes when Hoshijiro is
killed in action, and the Gauna absorb her body, later creating a powerful humanoid hybrid enemy known as Benisuzume, who retains Hoshijiro’s consciousness. This creates intense
emotional turmoil for Nagate, who fights not just for humanity's survival, but to save or put to rest the woman he loved. Culminating in massive, high-stakes space battles against overwhelming Gauna armadas, the narrative explores themes of sacrifice, identity, and the enduring human spirit. Nagate ultimately accepts his destiny as the Sidonia's ultimate protector, leading the defense against annihilation while unraveling the ancient mysteries tying humanity's past to the relentless Gauna menace, securing a precarious future for the last remnants of mankind drifting through the cold, unforgiving cosmos.