The novel begins by taking the real-world concept of Japanese yonige-ya, companies that help desperate people vanish and begin new lives, and turning it into a supernatural business. Haruto, a twenty-eight-year-old man with long silver-white hair, operates an elegant little stationery shop in Tokyo during the day. At night, however, the shop becomes the headquarters of his disappearing service. His clients are not ordinary humans but ghosts, forgotten gods, supernatural beings, elementals and even stories who need to leave the human world before they fade, are destroyed, or are consumed by creatures called Eaters. Haruto can see these beings and possesses a powerful form of paper magic: he animates origami cranes, creates boats and warriors out of paper and can even use paper doors to move through impossible spaces. His ultimate destination for clients is New Edo, a hidden refuge existing in the cracks between worlds. Time cannot normally enter New Edo, so nothing grows old, decays or truly changes there. Its inhabitants live beneath an eternal moon in floating houses on a river filled with living stories. New Edo also operates according to a strict principle of equality: gods may not build temples, fairies cannot establish kingdoms and nobody is allowed to elevate themselves above anybody else. Haruto belongs to a guild of night movers led by his severe mentor Yasu. Yasu has taught him that a night mover must remain detached, put the guild before personal feelings and obey every contract. Haruto is already beginning to question those principles. Early in the novel, for example, a god called Oda is condemned because he has violated New Edo’s rules. Haruto is supposed to take him on an elevator ride that will effectively execute him. Instead, Haruto gives Oda a chance to escape through one of his paper doors, not knowing whether the god will survive. At the same time, Haruto discovers something far more dangerous: time appears to be leaking into New Edo. Silver liquid seeps through a hidden cavern, and anything exposed to it begins ageing and decaying. Yasu orders him not to tell anybody, insisting that he has a plan.
The second main character is Umi Okashi-Visser, a freelance journalist carrying an enormous amount of unresolved family trauma. Umi and her twin sister Sora grew up partly in Amsterdam, where their parents ran a secondhand bookshop. Their mother Mako was brutally killed there, and their father Bram was convicted of her murder. Umi herself discovered the aftermath and has spent years believing that her father was a murderer. Afterward the twins dealt with the trauma differently: Sora became a sculptor, while Umi escaped into journalism, travel and other people’s stories. Eventually Sora grows increasingly withdrawn and then disappears entirely. The police classify her as a johatsu, a person who has deliberately evaporated from her old life, but Umi cannot stop looking for her. Four months after Sora disappears, Umi becomes interested in another disappearance, that of Take Kazama, a wealthy young jeweler whom she had previously interviewed. An origami crane found in Kazama’s office is identical to one Umi discovered in Sora’s studio. Following that clue brings her toward Haruto. Before meeting him, however, Umi discovers that the world is far stranger than she thought. Kazama’s former bodyguard Kenji takes her into the supernatural underside of Tokyo, where she sees grotesque Debt Collectors feeding on the blue light of forgotten gods. These beings notice that Umi can see them and call out her name. Umi also realizes that Sora had been sculpting supernatural creatures before she vanished, suggesting that Sora had seen the same hidden world. Umi eventually finds Haruto’s stationery shop and immediately suspects he is lying about Sora and Kazama. She follows him on one of his night-moving jobs involving Mrs. Kobayashi, a dead woman who is still chained to her grieving husband. Haruto discovers that the chains are not formed only from the husband’s prayers and inability to let go; Mrs. Kobayashi herself is clinging to him, meaning Haruto cannot simply cut her free. During the failed move, Eaters attack. Umi, who cannot see Mrs. Kobayashi’s ghost but can see the monsters, rushes in with a baseball bat and kills an Eater that is about to kill Haruto. Her blood attracts more of them. Haruto rescues her using his paper magic and concludes that she cannot safely remain in Tokyo. He offers to take her to New Edo. Umi agrees primarily because she believes Sora is already there.
The journey to New Edo is supposed to take a fixed amount of time inside a crack between worlds and then leave no physical mark on the traveler once they emerge. Instead, the deteriorating cracks turn Umi and Haruto’s trip into an enormous, dangerous detour that transforms both of them. Haruto gradually reveals his own history. He comes from a world in which fate is literally tattooed onto a person shortly after birth. A specialist called the Horishi inks a predetermined map of that individual’s profession, relationships, family and future onto the body. Haruto grew up learning the magical art of paper folding from his mother and eventually worked at a Museum of Education, where important moments in history were stored inside paper cranes. He was pledged by fate to marry a woman who loved somebody else. When authorities demanded that he betray the lovers, Haruto refused and was tortured so violently that his hands were smashed. He ultimately used his paper magic to help the couple escape, folded himself away from his persecutors and accidentally fell through a crack into New Edo. There Yasu trained him as a night mover. Haruto has therefore built his new identity around refusing attachment: after losing his home, his mother, his expected future and even his faith in fate, he convinces himself that wanting nothing is the safest way to live. Umi threatens that philosophy. During their journey they take shelter inside one of Haruto’s magical constructions, explore memories, talk, fight and slowly become emotionally dependent on one another. When the crack destabilizes further, one of Haruto’s paper doors begins transporting them not merely through space but through time. They first reach Haruto’s own past and witness his younger self after his hands have been destroyed. Umi wants him to intervene and alter what happened, but Haruto refuses. They are subsequently taken even further back to the moment when infant Haruto’s fate is tattooed onto him. Again Umi tries to interfere, and again Haruto insists that they cannot simply rewrite the past.