Thirty-two years have elapsed since the Invaders were defeated for the first time. A.E.G.I.S. has been mostly demolished, and it has evolved into an underground organization with just a few Gate Keepers remaining to defend mankind. Ayane Isuzu, one of the members, is weary of civilization as a whole, yet she continues to defeat the Invaders out of contempt for her father. Suddenly, she hears about the resurrected Machine General (Kikai Shogun) and Devil Count (Akuma Hakushaku), but they are accompanied by a mystery ghost girl. It is up to Ayane and the surviving members of A.E.G.I.S. to stop them and preserve mankind once more.