After Earth's destruction by enigmatic alien beings called Gauna, humanity seeks refuge aboard the vast generation ship Sidonia. Millennia later, the Sidonia faces renewed Gauna threats, prompting a desperate fight for survival led by the human-Gauna hybrid Tsumugi Shiraui and skilled mech pilot Nagate Tanikaze. A decade passes, bringing a semblance of peace to Sidonia. Amidst this tranquility, Tsumugi grapples with newfound emotions for the celebrated hero Nagate. Yet, Captain Kobayashi understands that the looming Gauna presence prohibits lasting peace. With humanity's fate hanging in the balance, a crucial decision is reached: a final, decisive battle to safeguard the remnants of mankind. As the decisive moment looms, can the crew defend their loved ones in the face of impending peril?