Yorito Morimiya is a young boy who loves taking pictures of the sky, and one day in the early morning while setting up to take a snapshot of the sunrise, he meets a strange girl. After talking with her for a few minutes, she disappears and is no where to be found. The next day, Yorito is coming back from buying some groceries on a rainy night and runs into the same girl; this time he finds out her name to be Matsuri Shihō. Later on, Yorito figures out Matsuri lives in a church and goes to find her. At the same time, Matsuri is being hunted by a mysterious man.

After the fight with Takeshi, Matsuri gets injured and Yorito tries to protect her by bringing her back to his home. After she wakes up, she tries to thank him by making him a meal, but due to her limited knowledge of the modern world, it does not work out. That night, Matsuri intended to leave Yorito's house without him knowing, but stayed to look at the sky painted on the ceiling of Yorito's room.

It has been a week since Matsuri started living with Yorito and he as become visibly suspicious to Mana who wants to find out what he is hiding. Mana comes over one night and tells him that she wants to make him dinner, though after he leaves to buy some seasonings, Mana tries to search the house. While initially unsuccessful, Mana runs into Matsuri eating in the kitchen and they become acquainted.

This episode mainly focuses on the friendship between Yorito's sister Aono and Mana's little sister Koyori, both of whom are staying at the hospital. Koyori, who is to be released soon, has trouble conferring this news to Aono. The relationship between Yorito and his sister is also explored, as more information about the dolls he brings her is revealed.

On a rainy, cloudy day, Matsuri and Yorito go outside and take a boat around the lake. Later on, Matsuri is ambushed by Takeshi in Yorito's home. Overpowered, she is about to give up as she notices the sky-painted ceiling in Yorito's room. This gives her the determination to fight back and flee the house, but only Yorito's eventual intervention prevents Takeshi from killing her.

Yorito finally decides to introduce Matsuri to Aono under the guise of her being his new girlfriend, but when they go to visit Aono, the latter feigns sleep. Later on, Aono meets with Matsuri in a tram depot where it is revealed that Aono is also a Yaka and her powers are now returning. Aono comes home with Matsuri and Aono tells Yorito that she has permission from the hospital to stay at home for now. After dinner, Matsuri and Yorito go to Yorito's school. At the roof of his school, Matsuri explains the loneliness of Yaka to Yorito. After that, Matsuri kisses Yorito and disappears.

Yorito and Mana search for Matsuri after she disappears on the night she kissed Yorito. Almost a month passes from Matsuri's disappearance, and Yorito has almost given up hope on her return. On a date out with Aono, Yorito accidentally runs into Matsuri again inside a convenience store and gives chase, leaving Aono alone. Yorito catches up to her to find out she has been living with Mayuko in an abandoned building. Aono is left wandering in the rain alone and is angered by Yorito's desire to be with Matsuri. Back in the abandoned building, Matsuri collapses after being stabbed by a piece of glass by a seemingly mentally vacant/unconscious Yorito who seems to be controlled by Aono.

Yorito wakes up one day in school believing that the night's previous events with Matsuri was a dream due to Aono intervening with her powers. Trying to remember what really happened, Yorito collapses in school and is taken home by Mana who is soon after told to leave by Aono. Yorito is kept in his room by Aono as she controls Yorito more with her powers in order to fulfill her desire to be with Yorito together.

Aono has come to kill Matsuri in an abandoned part of town and a one-sided battle ensues with Aono attacking while Matsuri runs for her life. In the end, Aono cannot bring herself to kill Matsuri and leaves afterwards. After suffering another mental attack, Yorito is brought to Mana's place to keep him safe from Aono who later comes looking for him; Mana manages to get her to leave. Later, Matsuri runs into Takeshi again who once again tries to kill Matsuri and nearly succeeds, but Mayuko intervenes in the end and saves her life.

Mana finally tells Yorito that Aono is a Yaka, but he initially does not believe her. He later confirms this after confronting his "sister" about what she is hiding from him, but Aono would not tell him. Yorito and Matsuri meet in the abandoned building where Yorito stabbed Matsuri in episode seven. Yorito asks her why he would have memories of hundreds of years ago, and Matsuri stabs him with Takeshi's sword to show him the truth. Yorito is not human, but a paper construct created by Aono with the memories of the Yorito from the past.

Yorito and Aono are planning on leaving so that things will go back to the way they were. Mana tries to get Yorito to tell her who he really is, but he does not say. Later, Mana is out with her friends and she brings up Yorito in conversation, but discovers that everyone else but her has already forgotten about him. Scared of what this means, Mana runs to the school roof and finds Yorito alone. After sunset, however, Mana finds herself alone on the school roof having forgotten about Yorito. Takeshi and Mayuko leave town near the end, and Matsuri goes to Aono's house with Takeshi's sword in hand.

Matsuri has come to Aono's house and go into a conversation about who Yorito chooses to go with — Aono to a different place, or Matsuri, whom he has asked a favor from. The two Yaka begin a battle in the wrecked construction area while Yorito waits in an old theatre. Just when Matsuri is able to deliver the final blow to Yorito and Aono, the old camera in the theatre comes on and displays the sky. Matsuri has a flashback and from what Takeshi said, drives the sword into her own self, much to the dismay and horror of the siblings.

Matsuri tries to forcefully stab Aono with her sword, but Aono moves out of the way in time; she still manages to get a wound on her shoulder. While Aono runs away, Yorito is left with an arm missing and he slowly becomes weaker since Aono is losing her Yaka powers. Matsuri tells Yorito to not intervene and goes after Aono. During the fight, Matsuri loses her sword, and Aono takes it up to shove it into Matsuri, but Yorito, not listening to Matsuri's heeding words, intervenes and he is impaled on the sword. Yorito then disappears in a flurry of paper followed by Aono's shrill cries. Matsuri does not hesitate this time to stab Aono and after the sun rises, Matsuri also disappears, but Aono is now human. One year later Aono comes back, and no one but she herself remembers who she is, or any of the incidents that happened. Aono meets with Mana and Koyori and they become friends again.