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.

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.

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.

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.