Summary
The leader of a secret government organization, Kunikida, is frantically searching for the young Kaede, who has escaped them. He cares for her as a father would, but her importance to Japan dictates that he must keep an eye on her at all costs. Kaede goes down into the ground, and refuses to return. Over the radio, Kunikida and his assistant hear Kaede say she wants to learn the truth about her destiny just before she vanishes in a beam of light.

A young girl named Momiji lives at a temple with her mom and grandmother. She cleanses herself in the sacred water at the temple daily, and has often been told that the day may come where she must sacrifice her life to save Japan. She doesn't really know the meaning of this though, for she assumes she is an ordinary girl. One day, on her way to school, she is confronted by an odd looking man named Mamoru, who seems tortured and tells her he must kill her. Momiji is saved by a few members of the secret government group. But, when told she is in danger, she refuses to go with them saying she is late for school. She attends school as normal, however, the school is attacked by a giant arigami. It chases after Momiji and captures her. She is momentarily rescued by Mamoru, who is still struggling with whether or not he can kill her. He finds that he can't do it, as his purpose is to protect the princess. The arigami recaptures Momiji and places her in a ceramic field. It explains that in the past, they had to protect the princess because if she dies, all of the arigami would die with her. That was why Mamoru was given the power and charged with protecting the princess with his life. But now, they have found that if they kill her within a ceramic field, they will not be destroyed. It attacks Mamoru first, but in order to save him, Momiji selflessly jumps in front of him and takes the brunt of the attack. Seeing that Momiji is no longer in the ceramic field, the creature places his soul on her wound in order to preserve her life. It then dies.

When Momiji returns home, she finds that her family has given her up to the government agency in order for them to protect her until the time comes when the arigami get to be to much, at which time, she, as princess will be a sacrificial lamb which will destroy them. She finds that she had a sister she never knew, Kaede, who was the girl that disappeared earlier. Although warned by Mamoru not to trust the organization because they will eventually be her executioners, Momiji decides to stay and help them as much as she can rather than sit back and wait to be just a sacrifice. Momiji finds that she has the power to detect arigami, and uses that power to aide the government organization, eventually becoming a full fledged member. Mamoru is constantly coming to her rescue, and she gradually falls for him. She finds out that Mamoru was in love with Kaede and once protected her as he now does for her. Although crude, rude, and not too nice at first, Mamoru comes to feel for Momiji as well, although he will never admit it.

The organization members become rather attached to Momiji and admire her courage, selflessness and kindness. A powerful arigami, in teem with Kaede, wakes an ancient arigami god in order to perform a ceremony to cleanse Japan of the humans which abuse the Earth. She views it as a chance to start over, however it means the death of the current population. Kaede succeeds in setting the ceremony in motion. Soon, the arigami plants are becoming too much, and all of Japan is threatened. The governor begins calling for Momiji's sacrifice. Momiji is torn between her wish to save the people, and her wish to live. She ends up trying another rout, and confronts her sister. Seeing that she is not willing to back down, Momiji begins to sing and initiates the same arigami destructive power which would have been achieved with her sacrifice. She keeps it up as she gets steadily weaker. Momiji's song seems to work, preventing the people of Japan from being killed by the plant's poisonous pollen. Her power of hope spreads all over Japan, but eventually she dies. Mamoru takes her in his arms and mourns her. Just then, Kaede appears and brings Momiji back to life saying that she will return again if she is needed. Japan now safe, Momiji and Mamoru travel back to her home. Momiji points out to him the spot where they first met.