Because she is a member of the Kushinada Clan and thus has the power to block Aragami, a girl named Momiji Fujimiya is destined to save Japan from destruction by becoming a human sacrifice. Mamoru Kusanagi, in turn,
was controlled by the Aragami via the imposition of a soul, "Mitama." His mission was to ensure that Kaede, who was Momiji's twin sister and possessor of the same unique power, was not turned over to the humans. The Aragami wants to capture Momiji and cut off the power of the Kushinada
Clan. Mamoru Kusanagi is now trying to protect Momiji instead of Kaede. There is also the special Land Control Center, part of the Prime Minister's Office Special Committee on Territorial Security.
The struggle takes place in Tokyo.