In 2563, a catastrophic war known as “The Fall” has left Earth devastated. While scouting the junkyard metropolis of Iron City, cyborg scientist Dr. Dyson Ido discovers a disembodied female cyborg with a fully intact human brain. Ido rebuilds the cyborg, who does not have any recollections of her past, and names her “Alita” after his deceased daughter.
Alita befriends Hugo, who dreams of moving to the wealthy sky city of Zalem. Hugo introduces her to the competitive sport of Motorball, a battle royale race wherein cyborgs fight to the death.
Alita discovers that Ido is a Hunter-Warrior when she follows him one night and they encounter three cyborg assassins led by Grewishka. When Ido is injured, Alita instinctively attacks the cyborgs, killing two of them and severely damaging Grewishka, who retreats underground. Despite Alita rediscovering her skill in the ancient martial art of “Panzer Kunst”, Ido discourages her from becoming a Hunter-Warrior. The next day, Alita finds and brings home a Berserker body from an old downed ship outside the city. Ido refuses to install her in the body, fearing the consequences of her heart’s full compatibility with it.
Fed up with Ido, Alita registers herself as a Hunter-Warrior, then she and Hugo enter the Kansas Bar to ask other Hunter-Warriors in helping her take down Grewishka, but they refuse, as Grewishka is not on the wanted list. Suddenly, an upgraded Grewishka storms into the bar and challenges Alita to a rematch, revealing that he has been sent by his boss, Nova, to destroy her. Despite her courage and combat skills, Alita’s body is sliced up by Grewishka’s bladed fingers before she blinds him with her left arm, and Ido, Hugo, and another Hunter-Warrior force him to retreat. Ido transplants Alita in the Berserker body, which automatically interfaces with her system.
Having fallen in love with Hugo, Alita enters a Motorball tryout race as a means to send Hugo to Zalem. Ido discovers that the other contestants are Hunter-Warriors and wanted cyborgs hired by Vector, an entrepreneur working under Nova, to kill her. He warns Alita, and as the race begins, she destroys many of the contestants with her superior skills. Meanwhile, Hugo is being hunted by a Hunter-Warrior named Zapan, after he frames Hugo for murdering a cyborg. Hugo calls Alita for help and she leaves the Motorball race to rescue him. She finds Hugo just as Zapan arrives and reveals to her that Hugo has been attacking cyborgs and stealing their parts for Vector for use in his Motorball games. Knowing that Alita is in love with Hugo, Zapan mortally wounds him and tells Alita that Hunter-Warrior law dictates that she must either kill Hugo or let Zapan finish him off. Chiren, Ido’s ex-wife and also a master cyborg engineer, manages to save Hugo by attaching his head to Alita’s heart. Zapan attempts to stop Alita from leaving and she slices part of his face off with his prized sword, which she takes with her.
Ido transplants Hugo’s head onto a cyborg body before telling Alita that Hugo’s actions were based upon the false belief that he would be able to eventually buy his way into Zalem. Ido confides that this was a lie fabricated by Vector, and that citizens of Iron City cannot enter Zalem unless they become Motorball champion. Alita decides to confront Vector, who is being mind-controlled by Nova, a powerful Zalem scientist. Through Vector, Nova reveals to Alita that Chiren has been harvested for her organs and then orders Grewishka to kill her. Alita battles Grewishka again and this time, thanks to her new body, finally kills him with ease, then stabs Vector, telling Nova that he made the mistake of underestimating her.
Ido tells Alita that Hugo has fled and is desperately attempting to climb a factory tube towards Zalem. Alita pleads with Hugo to return with her, but a massive spiked defense ring set off by Nova shreds Hugo’s body and throws him into the air. Leaping after him, Alita is unable to prevent Hugo from falling to his death, but not before he can thank her for changing him.
Months later, Alita is the star athlete of the Motorball tournament. As the crowd cheers, she points her sword towards Zalem while Nova watches her from above.