The film takes place in the year 2079. Forty-five years earlier, Earth was attacked by a hostile and implacable alien civilization from Alpha Centauri. Force shield domes are put in place to protect cities, and a totalitarian global military government is established to effect the war and the survival of humans. The Centaurians have never been physically seen.
The film follows Spencer Olham, a designer of top-secret government weapons. He is arrested by Major Hathaway of the Earth Security Administration (ESA), being identified as a replicant created by the aliens. The ESA intercepted an alien transmission which cryptanalysts decoded as programming Olham's target to be the Chancellor, whom he was scheduled to meet. Such replicants are perfect biological copies of existing humans, complete with transplanted memories, and do not know they are replicants. Each has a powerful "u-bomb" in their chest, which can only be detected by dissection or a high-tech medical scan, since it only assembles itself when it gets in proximity to its target. Detection via the special scan works by comparing against a previous scan, if there was one.
Major Hathaway begins interrogating Olham. As Hathaway is about to drill out Olham's chest to find the bomb, Olham breaks loose and escapes, accidentally killing his friend Nelson in the process. With the help of underground stalker Cale, Olham avoids capture and sneaks into the hospital where his wife Maya is an administrator to get the high-tech scan redone and prove he's not a replicant. But the scan is interrupted by security forces before it can deliver the answer.
Olham and his wife are eventually captured by Hathaway's troops in a forest near an alien crash site, close to the spot where they spent a romantic weekend just a week or so before Olham's arrest. Inside the ship they discover the corpse of the real Maya, and Hathaway shoots the replicant before she can detonate. Hathaway thinks he has killed the true imposter, but as his men move debris away from the Centauri ship, the real Spencer Olham's body is revealed. At that moment, Olham realizes aloud that he really is a replicant, and the secondary trigger (his awareness of what he truly is) detonates his u-bomb, destroying himself, Hathaway, his troops, and everything else in a wide area, in a fiery nuclear explosion.
In the final scene, the news announces that Hathaway and the Olhams were killed in an enemy attack, as if the government were covering up the truth or didn't know what actually happened. Cale wonders if he ever really knew Olham's true identity.