In a post-apocalyptic future, Dr. Dyson Ido, a compassionate cyber-physician, discovers the remains of a female cyborg in a junkyard. He salvages and reassembles her, naming her Alita after his deceased daughter. Alita awakens with no memory of her past and a new body. Exhibiting unique martial arts prowess, she ventures into Iron City, a sprawling metropolis where cybernetically enhanced beings coexist. Alita's kind innocence clashes with the brutal world around her, but she befriends Hugo, a young man who helps her navigate her new life.

As Alita strives to uncover her history, her emerging abilities attract the attention of powerful forces within the stratified society. The city is under the grip of the enigmatic Nova, whose influence reaches from the highest floating city of Zalem to the depths of Iron City. Alita's existence challenges the established order, setting her on a collision course with its defenders and the deadly sport of Motorball, a gladiatorial combat game that serves as both entertainment and a path to ascend to Zalem. She must engage in a battle not only for her own survival but also for the people she grows to love.