After a tranquil period back in her hometown, Yoshika Miyafuji is summoned by her ex-superior, Mio Sakamoto, to attend a medical school in Europe. Accompanied by Shizuka Hattori, a protege of Sakamoto, Yoshika heads back to Europe just as new Neuroi threats resurface. Soon, the dispersed members of the 501st Joint Fighter Wing start reuniting as a formidable Neuroi menace looms before Yoshika and Shizuka.