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5 years have passed, and not only has the land of Edo changed into an apocalyptic wasteland, but Kagura has changed into a beautiful woman with no Chinese speech pattern, Shinpachi has turned into a cool samurai who is not a tsukkomi anymore, and the Gintoki of this time has gone missing, though he is assumed to be dead. Gintoki is determined to find out the truth of the deadly sickness that is ravaging Edo, and also to understand the feelings of Kagura and Shinpachi, who have been trying to deal with their leader's disappearance.
Only the most powerful warriors are able to transcend their human bodies and become something even greater—samurai. Samurai carry special souls within themselves and can travel through space as easily as walking the earth. Hachimaru has always dreamed of becoming a samurai, but he’s as weak as they come. He’s so sickly that he can’t even eat solid foods. Being too weak to leave the house may have turned Hachimaru into an expert at video games, but with enough heart, could he become a true samurai?