Thirty-two years have elapsed since the Invaders were first defeated. A.E.G.I.S is now nearly dismantled, having devolved into an underground organization with only a handful of remaining Gate Keepers dedicated to saving humanity. Ayane Isuzu, one of the members, is fed up with society at large, yet she keeps defeating the Invaders out of spite toward her father. Suddenly, she discovers that the Machine General (Kikai Shogun) and the Devil Count (Akuma Hakushaku) have been revived, now accompanied by a mysterious ghost girl. It falls to Ayane and the remnants of A.E.G.I.S to stop them and save humanity once again.