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Serving as the grand cinematic conclusion to Tsutomu Nihei's sci-fi epic, the film follows the colossal interstellar seed ship Sidonia ten years after the start of its perilous voyage across deep space. Legendary Gardes pilot Nagate Tanikaze and human-Gauna hybrid Tsumugi Shiraui have fallen deeply in love, despite their vast biological differences. As Sidonia approaches the habitable planet Lem-VII to establish humanity's permanent new home, Captain Kobayashi detects the approach of the final Gauna hive, a monstrous agglomeration capable of crushing Sidonia. Tanikaze launches into the void to lead humanity's desperate last stand.
⚠ Background — may contain spoilers
The Gauna hive assimilates fallen Gardes, unleashing Ochiai's catastrophic bio-mechanical superweapon against Sidonia's defenses. Tsumugi shields the seed ship with her massive biological frame, suffering fatal injuries from anti-matter blasts. Grieving but resolute, Tanikaze pilots the upgraded Yukimori mecha straight into the Gauna mother core, detonating the Higgs weapon to annihilate the alien species permanently. Tsumugi's human brain consciousness is transplanted into an artificial human clone body, allowing her and Tanikaze to live together peacefully as a loving family on the newly colonized paradise surface of Lem-VII.
