Last Order was first published by Shueisha, Kishiro's longtime publisher, beginning in July 2001 and serialized in Ultra Jump. With Alita's Space Angels making it to the Finals and eventually triumphing, the stage is set for her to again affect the course of human history. The ZOTT, which takes place over the course of several days, eventually forms the primary story arc of Last Order as the motivations and backgrounds of additional teams are revealed while other events transpire in the background.
During the course of the story, more background about the setting of Battle Angel Alita that was not disclosed in the prior series is revealed, such as how the Earth emerged from a cataclysmic impact winter that wiped out most of humanity. Along the way, she forms an alliance with three of the former TUNED agents who have now begun to think for themselves, an unsavory superhacker, and Nova himself when she enters the LADDER-sponsored Tenth Zenith of Things Tournament (ZOTT), a Solar System-wide fighting tournament held every ten years. Going into space with new and old companions alike to rescue her lost friend Lou Collins and find out more about her forgotten past, Alita is caught up in an interplanetary struggle between the major powers of the colonised Solar System. The secret of Tiphares is publicly exposed and results in a brutal civil war, but Tiphares and the surface turn out to be a small part of a more complex world.
The story begins when Alita is resurrected by Nova's nanotechnology in the floating city of Tiphares a year later. Instead it takes place after Alita was killed by a doll bomb planted by Desty Nova. It ignores the transformation of Ketheres into a nanotechnological space flower, Alita's subsequent transformation into a flesh and blood human, and her reunion with Figure Four. Last Order continues from the final volume of Battle Angel Alita, but diverges from the original ending.