Yoshika Miyafuji is living a quiet life now that she is back in her hometown. Her former superior, Mio Sakamoto, has helped set up a place for her to study at a European medical school. Yoshika travels there with Shizuka Hattori, a former pupil of Sakamoto's from the naval academy. As fresh signs of the Neuroi appear, the 501st Joint Fighter Wing's former members, long scattered, begin to regroup. Then a powerful Neuroi confronts Yoshika and Shizuka.