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The storyline behind Blue Seed starts out simple and gets more and more complex as time progresses. Our heroine, Momiji Fujimiya, is an ordinary high school girl. She has been brought up by her mother and grandmother, all the time being taught ancient rites of cleansing. But little did Momiji know of the real reason for being taught those ceremonies. One day while walking to school Momiji is attacked by a strange, cat-eyed, orange skinned man with green hair and from then on nothing is the same. She is suddenly being chased by monsters that insist on calling her the Kushinada and is whisked away by a government agency called the TAC, or Terrestrial Administration Center. Momiji eventually learns that she is one of the twins born to the Kushinada family 15 years ago, and that only the Kushinada's death as a human sacrifice can stop the Arigami. Her tiwn sister Kaede has already been killed inside a special ceramic field that nullified her powers and now the Arigami want to do the same to Momiji. But Momiji and the TAC, along with the strange man Kusanagi who now protects her, aren't going to give up so easily!!

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