The central figure of the narrative is Alita, a female cyborg of formidable ability who is discovered in a state of suspended animation, her memory completely erased, amidst a vast scrapyard. Found by the cybernetic expert Daisuke Ido, she is rebuilt and given the name Alita, which was originally the name of Ido's late pet cat. Her true past is that of a Martian cyborg warrior originally named Yoko, a practitioner of a powerful lost martial art, though this remains a mystery to her for much of her journey. Her most identifiable trait is a fierce and unyielding determination, matched by a willingness to use overwhelming force when she deems it necessary. This warrior spirit contrasts sharply with her initial presentation as an innocent and curious teenage girl, a duality that defines her character. While known for her empathy and capacity to understand even her enemies, she is not a flawless paragon; she grapples with a disturbing potential for bloodlust and a deep-seated enjoyment of combat, which she sometimes uses as a coping mechanism for her internal rage and despair.

Alita's primary motivation is the rediscovery of her lost identity. She instinctively believes that through fighting, she can unlock the fragmented memories of her past life as a master of Panzer Kunst, the legendary cyborg martial art that begins to surface when she is threatened. Beyond her personal quest, she is driven by a powerful need to protect those she cares about, frequently putting herself in danger for her loved ones. Her sense of justice is personal and absolute, often leading her to directly confront the corrupt and powerful forces that exploit the weak in the dystopian world of the Scrapyard. Her famous declaration, "I do not stand by in the presence of evil," encapsulates her refusal to be a passive observer.

In the story, Alita occupies a central role as both a hero and a disruptive force. Starting as a newly revived amnesiac under the care of Ido, she quickly forges her own path by becoming a Hunter-Warrior, a bounty hunter who tracks down violent cyborg criminals. Her actions inevitably place her at the heart of the Scrapyard's most dangerous conflicts, from clashing with monstrous killers to becoming a star player in the brutally violent sport of Motorball. Her role evolves as she becomes entangled in the larger political and social struggles between the grounded Scrapyard and the floating utopian city of Tiphares, which exploits the world below. Her very existence challenges the established order, as she uncovers hidden truths and fights against forces that seek to control or destroy her.

Her key relationships are fundamental to her development. Daisuke Ido serves as her father figure and moral anchor, a scientist who rebuilds her and tries to protect her from the world's harshness, eventually learning to set her free to follow her own destiny. Her first love is Hugo, a boy who dreams of escaping to Tiphares, and his tragic fate deeply wounds her and significantly shapes her understanding of loss and obsession. She also shares a complex and evolving dynamic with the mad scientist Desty Nova, who shifts from being a primary antagonist to a trusted, albeit eccentric, ally. Later, she finds a more grounded and healthy romantic connection with a fighter named Figure Four, who helps her remember her humanity beyond being a living weapon. Through these connections, Alita experiences the full spectrum of human emotion, from love and joy to devastating grief, which continually reshapes her.

Her development is marked by a series of traumatic losses and physical transformations. She begins as an innocent, matures through the pain of Hugo's death, and descends into grief before finding new purpose in Motorball. Each time her body is destroyed, she is rebuilt in a new, more powerful form, progressing from Ido's original patchwork model to a fearsome Berserker body, a high-speed Motorball chassis, and eventually the advanced Imaginos bodies. These physical changes often parallel her psychological evolution, as she integrates the fragments of her past self, Yoko, and confronts the darker aspects of her own nature, including a "disturbing bloodlust". A significant moment of development occurs when she faces an existential crisis upon learning her brain has been replaced with a bio-chip, forcing her to question the very nature of her humanity, a crisis she ultimately overcomes to reaffirm her sense of self.

Alita's most notable abilities center on her mastery of Panzer Kunst, a hyper-lethal martial art developed for cyborgs in zero-gravity environments, which allows her to target enemy weak points with devastating precision and adapt to any combat situation. Across her different cyborg bodies, she possesses superhuman strength, speed, and agility far beyond ordinary humans and most other cyborgs. Her signature weapon is the Damascus Blade, an absurdly sharp sword that can cut through almost any material. She also demonstrates a high degree of resilience, surviving seemingly fatal destruction and being "repeatedly" resurrected, each time returning more powerful than before. Later in her journey, she also gains access to more exotic powers, including the manipulation of nanotechnology and chi, which allows her to read her opponents' intentions an instant before they act.