It has been 32 years since the Invaders were initially defeated. A.E.G.I.S has now become a clandestine organization with only a handful of Gate Keepers remaining to protect humanity. Ayane Isuzu, one of the members, is disillusioned with society but continues to battle the Invaders in honor of her father. However, her world is turned upside down when she discovers that Machine General (Kikai Shogun) and Devil Count (Akuma Hakushaku) have been revived and now have a mysterious ghost girl by their side. Ayane and the remaining members of A.E.G.I.S must band together once more to save humanity from their impending destruction.