In the early Meiji era, Himura Kenshin, the former assassin Hitokiri Battosai now wielding a reverse-edged sakabato, resides at the Kamiya Kasshin-ryu dojo in Tokyo. His peaceful life training under instructor Kaoru alongside young Yahiko is disrupted when Tae, a waitress from the Akabeko restaurant, arrives with a request for help.

A regular customer named Okuma Daigoro has lost a precious book belonging to his master, Katsu Kaishu, a significant figure from the previous Shogunate era now serving in the New Government. The stolen item is a translated copy of Jules Verne's From the Earth to the Moon, a title that hints at themes of science and distant voyages. While the search for the missing book begins as a simple favor, Kenshin quickly perceives that the true stakes are far greater. The cloth wrapping the book contains a secret message, and its theft threatens to expose Kaishu to accusations of hiding war funds from the Tokugawa regime.

The investigation pulls Kenshin and his friends into a dark plot involving the Beni Aoi, a faction of former shogunate guards seeking to overthrow the Meiji government. The situation escalates dramatically when Kaishu's daughter, Itsuko, is kidnapped, with her safe return demanded in exchange for the hidden Tokugawa gold. This conflict sets the stage for Kenshin to directly confront the Beni Aoi, utilizing his swordsmanship to protect Itsuko and unravel the conspiracy tied to the Verne novel.

The light novel presents two distinct narrative arcs. Alongside the main mystery is a second story focusing on Sagara Sanosuke, Kenshin's brawler companion. While running an errand to buy a nishiki-e woodblock print, Sanosuke is stunned to discover a depiction of his former commander, Captain Sagara Sozo of the Sekiho Army. This leads him to the artist, Tsukioka Katsuhiro, a former comrade. Their reunion becomes troubled as Sanosuke learns Katsuhiro has spent a decade planning a violent act of revenge against the Meiji government for their betrayal and the execution of their captain, a path that ultimately forces Sanosuke to confront his own loyalties and the nature of justice in the new era.