13 years ago, suddenly one part of Tokyo broke off and began to float in the sky. Tokyo was separated into "Old Tokyo" as the part that was floating in the air, and "New Tokyo," the part that stayed on the ground. Communication and interaction between the two Tokyos was impossible, and years passed. One day, a young girl perceives that Old Tokyo will fall back down to the ground, and she sets out on the perilous path from from Old Tokyo to New Tokyo to save the citizens from the impending crisis.
The story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war's aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section's Daisuke Aramaki encounters Motoko Kusanagi, the cyborg, wizard-level hacker assigned to the military's 501st Secret Unit. Batou, a man with the "eye that does not sleep," suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute's murder. Motoko herself is being watched by the 501st Secret Unit's head Kurutsu and cyborg agents.
In a quicksand surrounded town called Makka, rumors spread of a legendary robber named Gasback is after the town. To protect it, Mayor Kepler has hired bounty hunters. These hunters have been following Gasback from town to town in hopes of getting the bounty. Vash the Stampede is in town, along with Meryl and Milly, along with the female bounty hunter Amelia and Nicholas D. Wolfwood.
