In ancient Japan, there lived a princess (Can you tell why I like this show?) of the Kushinada family who was to be sacrificed at Izumo to the head Aragami, Yamata-no-Orochi (Eight Headed Hydra). However, she was saved by the outcast god, Susano-oh, who defeated the Aragami (the kanji translate to "wild gods") and won her heart.

For some time, the Aragami were unable to enter the human world, but this did not last forever. Throughout the ages, whenever the Aragimi began re-appearing in the human world, the Kushinada have used their powers to protect Japan. But with this power comes a high price: in order to generate what will be called the "Kushinada pulse", the Kushinada must die. This act locked the Aragami away, but never for good.

Around 15 years before the start of the series, twin sisters (Momiji and Kaede Fujimiya) were born into the Kushinada family line. This event re-awakened the Aragami, who began entering Japan and wreaking havoc, allowing for the formation of the TAC (Terrestrial Administration Center), a secret government organization created to destroy the Aragami.

At birth the two sisters were separated, Momiji growing up with her mother and grandmother at a temple and Kaede, under the protection of Daitetsu Kunikida (head of the TAC), where she recieved training of her psychic abilities. Upon her sister's death, Momiji is forced to take Kaede's place with the TAC and do whatever it takes to get rid of the Aragami for good.

Momiji is also protected by Mamoru Kusanagi a human/Aragami hybrid created by Yamata-no-Orochi, an Aragami, in order to protect the Kushinada from harm... at least until the Aragami find a way to trap her in a ceramic field and kill her safely. Kusanagi, who is seen as an outcast of both worlds (human and Aragami) first tries to kill Momiji in order to be free from his Aragami masters, but he later sides with Momiji and the TAC in their fight against the Aragami.