In the year 2563, exactly 300 years after Earth was devastated by a catastrophic war known as "The Fall," Alita talks to Dr. Dyson Ido in his workshop before her final Motorball game which will make her eligible to enter Zalem.
Dr. Dyson Ido explains to her that it will be too difficult to defeat Nova on her own.
"He most likely has a large security force protecting him on Zalem," says Ido.
Alita returns to the old, underwater, URM ship to search for clues to a possible solution in defeating Nova. Unable, to find anything of value she gets curious about where the ship came from. She activates the ship's black box to view its original mapped trajectory. The initial launch point shows an area 381.9 miles east of Iron City, in a desert. She estimated it would be a 4-hour trip using a jet hovercraft.
Alita travels to the desert location, but the launch point is barren. She uses a radio wave musical code she attained from the sunken ship which is used to locate hidden URM ships and military bases.
After playing the melody, a hidden elevator rises out of the sand. She takes the elevator and finds herself in an underground military command base with several dozen ships, a large fuel supply, various types of weapons, and a supply of ammunition. While inspecting the facility she discovers 400 URM soldiers in hibernation sleep.
Alita taps her fingers on a translucent control panel and wakes them from their sleep. The leader of the unit tells her that they are the reinforcement for the battle against Zalem.
She tells them the battle for Zalem was lost 300 years ago, and her commander wasn't able to activate the reinforcement.
Alita tells them that she needs their help to destroy Nova.
She explains, "After I'm accepted into Zalem, I plan to deactivate the defence ring on the supply tube, so that your unit can climb the tube to fulfill our quest to destroy Nova."
After winning the Motorball games, Nova signs an order to accept Alita into Zalem. She's asked to prove her loyalty to the city of Zalem by fighting as a gladiator in Zalem's coliseum. After beating three difficult opponents she gets an audience with Nova who tells Alita that she has met all of his expectations and he wants her to be his apprentice, so she can help him to rule Zalem under his political theories. Nova tells Alita that he wants to make her general of his droid army. He confides in her that he suspects someone in Zalem is leading a rebel force against him, but he's having a difficult time finding them.
Zapan enters the room and is instructed by Nova to give Alita a tour of the city. While on tour Zapan and Alita are attacked by rebel assassins. Zapan saves Alita's life and they fall in love with each other. Alita's outlook on life converts Zapan into a kind and loving individual. When they tour Nova's droid factory she discovers that her Panzer Kunst instructor, Gelda, and three URM soldiers are still alive, and they are working as slaves buildings military droids.
Alita secretly follows Gelda to her flat and they talk. Gelda explains that she is the commander of the hidden rebel army on Zalem and very soon they plan an attack on Nova. Alita tells Gelda that she saw thousands of droids being constructed, but she hasn't seen a single one walking around Zalem. Gelda tells her that Nova has been shipping the droids to a secret military base on earth to build an army to keep Iron City under control, and he hopes to use the droid army against the colony on Mars to conquer a new home for the growing population of Zalem.
The rebellion breaks out and Nova summons Alita to his laboratory. He tells her that he has a reserve of 500 droids on Zalem and he has released them on the rebels. He orders Alita to aid the droids in destroying the rebellion. Alita leaves and hides from sight, waiting for Nova to leave, she then breaks into his lab and destroys the control panel for the defense rings. Alita then sends a signal to the URM reinforcement, waiting in Iron City, to join the rebellion. Zapan, no longer a hunter warrior, joins the rebellion to help Alita free the innocent people of Zalem.
After the droids on Zalem lose the battle, Nova escapes on a ship with a group of upper-class elite who have kept Nova in power through rigged elections. They head to the secret droid military base on Earth to join 500,000 droid soldiers, to retake Zalem.
Gelda orders Alita and the rebellion to attack Nova's military base on earth. She tells Alita that hidden on the moon there is an URM army of one million with ships and weapons. They were ordered to guard the DNA codes of three million URM people who are to be used to establish a settlement on the earth, in the future. They also guard URM scientific researcher's who are advancing URM technologies. She tells Alita that she will take a ship and head to the moon to ask the URM army to help her against Nova's droid army on earth.
During the battle at Nova's military base, the rebels are at the point of losing the battle when they hear a large explosion and they see that the entrance to the base has been blown away. A million URM soldiers enter along with two million blue-colored URM droids. Within an hour the battle is over and Nova loses. Alita finds Nova crushed under an URM military vehicle. He looks at Alita and his last dying words are, "I made a mistake for underestimating you; I didn't see this coming."
After Nova dies, a chip in his brain sends out his memories through a wave signal to the mind of a hibernating clone on Zalem. Nova is reincarnated and quickly enters a ship and heads to Venus in hopes of getting political asylum.
The people of Zalem and the URM people from the moon join the humans of Iron City to live together in peace as one unified race on earth, creating the last kingdom.