After a harrowing encounter with a massive Gauna that costs many lives, Kobayashi, the captain of the spaceship Sidonia, undergoes a political transformation. Seizing control, she sets out to eliminate the Gaunas from the Lem system, where Sidonians have established a new colony. Bolstered by advanced anti-Gauna weapons and the powerful human-Gauna hybrid Tsumugi Shiraui, Kobayashi faces resistance due to prejudices against chimeras and the uncertainty of her military campaign. Seeking assistance from elite pilot Nagate Tanikaze, who shares a unique connection with Tsumugi, Kobayashi prepares for the ultimate showdown. Amidst the looming battle, Tanikaze cherishes peaceful moments with his friend Izana Shinatose even as Kobayashi harbors a dangerous secret weapon project that could jeopardize Sidonia's future.