In a dump in the lawless settlement of Scrapyard, far beneath the mysterious space city of Zalem, disgraced cyber-doctor Daisuke Ido makes a strange find: the detached head of a cyborg woman who has lost all her memories. He names her Alita and equips her with a powerful new body. While Alita remembers no details of her former life, a moment of desperation reawakens in her nerves a legendary martial arts ability.

Regrown, she decides to become a hunter-killer, tracking those who prey on the weak. But can she hold onto her humanity as she begins to revel in her own bloodlust?