Momiji Fujimiya believed she was an ordinary girl who lived in Izumo Japan, the place where all myths started. One day, a strange tall man with 7 little blue seeds confronted Momiji and claimed she is the Kushinada princess. He also claimed that he came all the way to Izumo to kill her, since her long lost twin sister was dead already.
Momiji, who was confused, was interrupted by sudden attack of the Yamata-no-Orochi, who was an Aragami demon. The strange man who wanted to kill Momiji earlier, suddenly saved her from this Aragami. Later, Momiji learned that the strange man was named Kusanagi. Before the Yamata-no-Orochi dies, it shot a vine right through Momiji's chest, leaving a 'mitama', or blue seed, attached to her chest.
After the attack of the Aragami demon, more and more other Aragami starts to invade Japan. The Terrestrial Administrative Center (TAC), a group of people who specializes in exterminating the Aragami, came and protected Momiji who was known as princess kushinada to them. Along with the TAC and Kusanagi, who decided to protect her instead of killing her, Momiji goes through many dangerous missions and illiminates the Aragami's.
After a long period of Aragami fighting, Momiji develops strong relationships between the TAC members and, especially, Kusanagi. She later falls deeply in love with him, but have many problems to confess love to him. But who would've guessed Momiji's long lost sister, Kaede, would appear with Murakumo and Susano-oh and completely changes the fate of Japan??