The story revolves around Suzuhara Izumiko, a girl raised within the confines of Tamakura Shrine, one of the Kumano shrines that are part of a World Heritage site. However, after Izumiko spent practically her entire life at Kumano until middle school, it was decided that she and her childhood friend Miyuki would enroll in Houjou High School in Tokyo. On a school trip to Tokyo, a mysterious entity known as Himegami appears and a terrible incident occurs. Izumiko's family carries a great secret that Izumiko is about to learn.
One day Izumiko decides to cut her bangs as her first step toward self change. Despite her best efforts, she is still the center of bullying at school. To make matters worse, the new transfer student is an old acquaintence who seems to hate her.
Izumiko and Miyuki plan to see Yukariko during their fieldtrip in Tokyo. Upon arriving in Tokyo, Izumiko begins to sense something sinister following her. Miyuki thinks it's all in her head until a series of events prevent them from seeing Yukariko.
Wamiya has noticed a change in Izumiko since her brief trip to Tokyo. When it becomes clear that Izumiko no longer hates Miyuki, Wamiya realizes that he is the cause of her change. Wamiya decides that it's time to wipe Miyuki out of the picture.
On the first day of school, Izumiko starts to see black figures around campus. It becomes apparent that Izumiko and Miyuki they aren't the only students with special powers. While some seem to be friends, others have taken a more aggressive stance.
Mayura and Manatsu decide to retaliate against Takayanagi and invite Izumiko and Miyuki to watch. People of power are beginning to gradually take an interest in Izumiko, including the secret Student Body President.
Izumiko and Miyuki visit the Souda abode before attending a camping trip in Togakushi with the Student Body Council's Executive Committee. While on the trip, Izumiko begins to catch glimpses of the hardships that Manatsu and Mayura must endure.
Mayura and Masumi put Miyuki to the test, refusing to believe that he is an inexperienced Mountain Monk. After the trial, Manatsu receives a call that Tabi is sick. Manatsu rushes to his beloved horse's aid, but things don't look good...
After losing Tabi, Manatsu decides that it is time to leave Mayura and become one with Masumi. He thinks that it would be easier on Mayura if they both left her now, before she grows too attached to them. Can Izumiko make them change their minds?
The battle between Mayura and Takayanagi is starting to get intense. As Mayura's trump card, Izumiko needs to exercise caution, but she's entering a rebellious stage. What will happen when she dresses up like a princess and unbraids her hair...?!
Strange things are happening at the school festival. The middle school girls refuse to dress up as princesses for fear of a curse and several of the girl students who have visited the Horror House have gotten sick. Could Takayanagi be behind this?
Takayanagi places a spell on Izumiko that makes her believe that she is his ally. Even so, she keeps finding herself revolted by Takayanagi's schemes. Will she be able to realize that something is amiss and break the spell on her own?
Realizing that she is the Hime-gami, Izumiko vanishes deep into an alternate plane. Miyuki, Takayanagi and Wamiya go after her, but a powerful enemy stands in their path! Can the three reach Izumiko before humanity's fate is sealed?