In 2043, a humanoid artificial intelligence terrorist named Harlan leads a devastating war of machines against humans, resulting in 3 million deaths. The military forces of the newly formed International Coalition of Nations (ICN) eventually drive Harlan into outer space after a series of victories.

Twenty-eight years later, Atlas Shepherd, an analyst with a deep-seated distrust of AI and the daughter of Harlan’s designer, is determined to track down the fugitive. After capturing one of Harlan’s AI agents and extracting information, Atlas learns that Harlan has escaped to a planet in the Andromeda Galaxy. She insists on joining the military mission to capture him.

As the ICN Rangers prepare to descend to the planet, Harlan’s drones launch a surprise attack on their orbiting ship. To survive, Atlas enters a mech and falls to the planet, where she gains basic control of the mech with the help of its onboard AI, named Smith. After discovering her team dead at the drop point, Atlas reluctantly interfaces her mind with Smith for better control. During their journey towards a rescue pod, Atlas bonds with Smith and reveals that her mother created Harlan.

Despite running low on power, Atlas persuades Smith to locate Harlan’s base and tag it for a strike. However, Harlan hacks Smith and captures Atlas, revealing his plan to destroy most of humanity and guide the survivors under AI rule. Harlan extracts security codes from Atlas’s brain to bypass Earth’s defenses and steal a ship with carbon bombs to incinerate Earth’s atmosphere.

Atlas, left to die with Colonel Banks, uses Banks’ neural interface device to reactivate Smith and escape. She reveals to Smith that Harlan killed her mother after she allowed Harlan an unfettered interface with her mind, leading Harlan to perceive humanity as a risk. Smith helps Atlas overcome her guilt, and with Banks’ sacrifice, they destroy Harlan’s ship and defeat Harlan in combat. Smith shuts down, and Atlas is rescued after multiple defibrillations.

Back on Earth, Atlas learns that analyzing Harlan’s complex CPU will take years. Now a ranger, she tests a new mech model with her modifications. As the mech boots up, its AI echoes a phrase from their mission and asks Atlas to guess its name, hinting that the Smith program has survived.