Shinpachi and Kagura, Gintoki's Yorozuya friends (or rather, employees facing labor violations), continue to scrape by in Edo's futuristic, alien-infested city. They take whatever work they can get their hands on while avoiding anything too dangerous. When Katsura, the leader of the Joui rebels and a long-time acquaintance of Gintoki's, goes missing after being brutally attacked by an unknown assailant, Shinpachi and Kagura launch an investigation into his whereabouts and the assailant's identity. Meanwhile, Gintoki takes on a seemingly unrelated task: the blacksmith Tetsuya has asked Gin to recover a strange and powerful sword known as the Benizakura that has been stolen recently.The Yorozuya crew finds themselves in the middle of a major conspiracy centered on the sinister nature of the Benizakura sword as the two investigations gradually intersect. Gintoki decides to take the fight straight to the enemy's headquarters, and sets out on one of his most dangerous missions yet with the help of a few unexpected allies.