In a mythical world where humans and gods co-exist, a ceremony marking the new governing princess is about to occur for the first time in 60 years. Only a girl from the Hime Clan may take this position, but the lack of females born to this family means that a boy called Arata must pose for the role. During the ceremony, the Twelve Shinsho, the wielders of special swords called Hayagami, led by Kannagi, betray the princess by trying to kill her and Arata. Arata escapes and runs into the Kando Forest. He emerges from the forest and finds himself in the alley in present day Japan. He has a run-in with the police because he is shirtless but is saved by Nao, a girl who claims to be his sister....