The story takes place in Edo, Japan, which has been taken over by aliens (Amanto). The samurai of Japan have all fallen since the Amanto placed a ban on carrying swords in public. The story focuses on an insane samurai with a natural-perm, Sakata Gintoki, his (partial) apprentice who he framed in the first chapter, Shimura Shinpachi, and a teenage girl from the "Yato" clan, Kagura. All are "freelancers" who search for work in order to pay the monthly rent, which usually goes unpaid anyways.