In a post-apocalyptic world, a vast technologically advanced city known as Tiphares floats above the slums of society known as the Scrapyard. Life in the Scrapyard is less than secure, many people becoming cyborgs due to injuries, for protection, or to better suit themselves or profession. There indeed are many dangeous job positions to fill, most notably being those of the hunter warriors.

Things in the Scrapyard were too unrully, the police and other organized law enforcement soon being torn assunder. Now the law enforcement of the land are bounty hunters who prefer to be addressed merely as hunters. Most Hunters are cyborgs, though there are some exceptions. When registered as a hunter, your identification barcode is stamped onto your brain (hey, you don't use all of it, and what else is permenant on a full cyborg?). Hunters claim their bounties by retrieving their prey's heads and collecting the reward upon disposal. Not the sort of work everyone would do, ne?

It starts out with one doctor mechanic hunter warrior named Ido Daisuke scavenging the junk yards of the Scrapyard. On this particular day though, he finds something amazing- an old cyborg's torso with a functioning brain! Quickly he takes it back with him and awakes the cyborg, but she has no recollection of her past. Ido dubs her Alita (after his faithful, male cat who'd passed away the month before) and starts rebuilding her a body. The story takes off from there.

Alita soon discovers Ido's after hours job and becomes a hunter warrior herself against his will. He allows her to sign on however; he didn't want to stand in the way of Alita's dream, and also he realizes early on that she knows the art of Panzer Kunst, rumored to be the most powerful cyborg martial arts technique ever developed. After shattering the first body Ido gave her in a brutal fight, Alita gets hooked up to a Berserker body. It's technology is fairly advanced compared to normal scrapyard components, and it's battle capabilities are extreme. By rediscovering the depths of her knowledge regarding battle and the Panzer Kunst technique, Alita hopes to one day rediscover her true identity.