Decades after the Invaders' initial defeat, A.E.G.I.S has crumbled into an underground faction with a handful of Gate Keepers striving to protect humanity. Ayane Isuzu, fueled by disdain for society and a vendetta against her father, reluctantly continues battling the Invaders. When news emerges of the reemergence of Machine General and Devil Count, accompanied by a cryptic ghostly girl, Ayane and the remaining A.E.G.I.S members must thwart their plans to safeguard humanity from impending doom.