After leading a peaceful life in her hometown, Yoshika Miyafuji is offered the chance to study medicine abroad in Europe by her former superior officer, Mio Sakamoto, and a group of others. Yoshika returns to Europe with former naval academy student Shizuka Hattori, who was mentored by Sakamoto. However, they soon become aware of new threats posed by the Neuroi. This prompts the disjointed members of the 501st Joint Fighter Wing to come together again. In the end, Yoshika and Shizuka must face off against a formidable Neuroi.