The 501st Joint Fighter Wing is disbanded with the unveiling of the unmanned anti-Neuroi unit, Warlock. As the Witches scatter, something goes very wrong during the Warlock's sortie against the nearby Neuroi hive.

Yoshika launches alone against the out-of-control Warlock, desperately holding out as the other Witches race to join her and put an end to the monstrous hybrid of human and Neuroi technology.

Yoshika's plans to become a doctor are put on hold after a mysterious letter from her father leads to a reunion with Sakamoto. Elsewhere, her former Strike Witch comrades take to the air to battle a new breed of Neuroi!