The movie begins with most of the earth destroyed and being run by the Psychlos (Aliens). Travolta is the head of security for the Psychlos.
Jonnie Goodboy Tyler is captured after leaving his mountain village to investigate the stories of monsters inhabiting the earth. Travolta notices his intelligence and wants to train Jonnie to mine gold. He artificially increases Jonnie's intelligence. Travolta wants Jonnie to illegally mine gold, but in reality, Jonnie is using his time to obtain weapons including jets and an atomic bomb to lead a revolt.
The plan is to blow up the glass dome that the Psychlos live in so the earth's atmosphere will kill them. The atom bomb is going to be tele-transported to the Psychlo's home world. The atmosphere of the Psychlo's home world, interacts with radiation so they figure that one atom bomb will destroy their whole world.
Jonnie enters the dome, sets the earthlings free and after a long battle, using US Military jets, the dome is shattered, the alien home world is blown up and John Travolta is captured.
The final scene has John Travolta in jail surrounded by the gold from Fort Knox. They have not killed him because if other outposts of Psychlos exist, they will trade him for their safety.
Travolta's 2nd in command (Forest Whitaker) is aiding the humans, showing them how to use Psychlo technology.
Spoiled by: The Movie Spoiler