Hana Kuroda, a skilled paper restorer in Kyoto, lives a solitary life consumed by her work and grief for her brother Kenji, a talented origami artist who died three years ago. Her routine is interrupted when Father Gabriel Serrano from the Vatican Library approaches her with a mysterious document—an intricately folded paper structure called a hyōgu no origami, designed to protect ancient secrets through elaborate puzzles. Together with Akio, an eccentric origami master who was Kenji's teacher, they decipher the document's hidden text, learning it was created by Brother Ichiro Tanaka, a 17th-century Japanese Jesuit. The puzzles lead them to an abandoned imperial garden concealing a secret underground chapel.