In the year 3000, Earth has been ruled for 1,000 years by the Psychlos, a brutal race of giant humanoid aliens. The remnants of humanity are either enslaved by the Psychlos and used for manual labor or survive in primitive tribes living in remote areas outside Psychlo control. Jonnie Goodboy Tyler (Barry Pepper), a member of one such tribe, leaves his home in the Rocky Mountains on a journey of exploration. He joins forces with Carlo (Kim Coates), a hunter, but both men are captured by a Psychlo raiding party and transported to a slave camp at the Psychlos' main base on Earth, a giant dome built over the ruins of Denver, Colorado.
Terl (John Travolta), the Psychlo security chief on Earth, has been condemned by his superiors to remain indefinitely at his post on Earth as punishment for an unclear incident involving "the Senator's daughter." Aided by his deputy, Ker (Forest Whitaker), Terl devises a plan to buy his way off the planet by making a fortune using human slaves to mine gold in radioactive areas. Psychlos are unable to visit such areas due to the explosive interaction of the gas that they breathe with radionuclide particles. Terl selects Jonnie as his "foreman" for the project and gives him a Psychlo education using a rapid-learning machine. Terl gives Jonnie a party of slaves and a Psychlo flying shuttle and orders him to go out and find gold.
After learning the Psychlos' language, history, and myriad other educational forms from the rapid learning machine, Jonnie plots a human uprising against the Psychlos. He obtains gold from Fort Knox to satisfy Terl's demands, instead of mining gold as ordered. Jonnie and his followers find an abandoned underground US military base with working aircraft, weapons, fuel, and nuclear weapons. They use the base's flight simulators to train themselves in aerial combat.
After a week of training, the rebels launch a mass uprising against the Psychlos using Harrier jump-jets and other weapons. Carlo sacrifices himself to destroy the dome over Denver, and the Psychlos inside suffocate in Earth's atmosphere, which they are unable to breathe. Jonnie captures a Psychlo teleportation device and uses it to teleport an atomic bomb to the Psychlo home world. The ensuing detonation causes the entire Psychlo atmosphere to explode, wiping out the planet. Ker and Terl survive on Earth but face different fates: Ker sides with the victorious humans, while Terl is imprisoned as a hostage within a vault in Fort Knox. The film ends with the humans in control of Earth but facing an uncertain future.