It is the 16th year of the Meiji era. Five years have passed since Kenshin Himura stopped the uprising of Makoto Shishio. Though the flames of his budding revolution were extinguished, the scars left in its wake are still felt across Japan. Remnants of his group—though scattered—still exist. Some have found peace while others continue to fight.

After a remaining faction tried to revive the revolution, Shishio's old sword fell into the hands of Ashitarou Hasegawa, an orphan boy who has never known a home. The conflict also leaves both Aran Inoue, a 16-year-old half-Japanese, half-American boy, and a mercenary girl named Asahi Kubota with a hefty price to pay off, with nowhere else to go. But luckily for these individuals, the Kamiya dojo has always been a place to accept wanderers without prying into their pasts.

The three are keen to start fresh, so when two members of Asahi's former clan show up demanding her return, Asahi refuses and things start to get ugly. In the midst of the chaos, the clan members drop a package containing a picture of dojo proprietor Kaoru Kamiya's presumably deceased father and his location—Hakodate, Hokkaido. With only this information, the members of the Kamiya dojo embark on an adventure across the sea in the hopes of finding news about Kaoru's father and the reason he is being targeted.