Chapter 1: Priest Myoue and his wife, Koto, and three children, live in Enzanji temple in Kyoto. The people around them find them creepy, so they decide to move to the Looking Glass City. Chapter 2: The family is happy, but Koto has a dream where disaster strikes the city, so the parents leave their children behind.

Chapter 3: With the parents gone, the children are left to run the city for themselves. One day, a girl called Koto appears.

Chapter 4: In the past, Koto lived with Inari, who worked for the Chief Priest of the shrine and was also her teacher. Chapter 5: She realized that Inari may be her real dad, and that the black rabbit in the picture may really be her mother, but kept it a secret. Chapter 6: In the present Looking Glass City, the Council of Three thinks that Koto's red eyes may be a sign of their mother's return

Chapter 7: Kurama, the de-facto ruler of Looking Glass City, tells Koto that their mother is the black rabbit. Chapter 8: Kurama has been intellectually curious from a young age, and loved it when his father praised his inventions. He wants to find what he can do outside of the Looking Glass City. Chapter 9: The identities of Doctor Shouko and Fushimi are revealed...

Chapter 10: The Station Opening, the day when everyone in the city gets rid of what they don't need, begins, and a cup that is very important to Yase is thrown away. Chapter 11: Yase has lived her whole life surrounded by things that remind her of her mother, and Koto tries to get her cup back, but... Chapter 12: Koto tries to fix things between Kurama and Yase, and feels a connection to her mother between them.

Chapter 16: Yakushimaru was saved by the Priest Myoue from the flames, and became a member of his family, but... Chapter 17: As time passed, Myoue began to believe that Koto really was their younger sister, but when he sees the picture of Inari he's struck by how little it looks like the Priest he knows. Chapter 18: Meanwhile, Kurama and Yase have Koto fight Bishamaru, hoping to use Aratama's energy to summon their mother.

Chapter 19: Koto takes her mother from the Shrine's Holy Grounds to the Looking Glass City. Chapter 20: The three siblings enjoy their time with their mother, but... Chapter 21: Koto tries to find out the secret of her birth from her mother, but instead she's asked to save her poor father. With no place for her feelings to go, she takes them out on Myoue.

A shock wave and asteroid strike the Looking Glass City as the people run and the town beguns to collapse. This was caused by Koto's use of Aratama. The Shrine and Chief Priest appear, and the truth of the city is revealed... Koto says that if they don't save the city and the people, she'll destroy everything.

Inari is moved by Koto's desire to know the truth of the looking glass city, and starts to tell her the secrets of the universe. When he's done he stabs her with his sword. The others are shocked. Koto's Aratama explodes and the world is destroyed. Myoue confronts Kurama and Yase amidst the rubble. Myoue awakens as the true king of the city, and runs to stop the end of the world.

Inari asks Koto why he exists, and tells her to live because he's going to disappear. Myoue and Koto use the prayer beads to try and restore the city, but are sent to heaven where they meet God and are told to become the new masters of the Looking Glass City. Koto confronts Inari in the Holy Grounds to find his true intentions and the answer to everything.