In the year 2019, Lincoln Six Echo and Jordan Two Delta live with others in an isolated compound. Their community is governed by a set of strict rules. The residents believe the outer world has become too contaminated for human life with the exception of one contagion-free island. Every week, a lottery is conducted and the winner gets to leave the compound to live on the island.
Lincoln begins having dreams that he knows are not from his own experiences. Dr. Merrick, a scientist who runs the compound, is concerned and places probes in Lincoln's body to monitor his cerebral activity. While secretly visiting an off-limits power facility in the basement where his friend, technician James McCord, works, Lincoln discovers a live moth in a ventilation shaft, leading him to deduce the outside world is not really contaminated. Lincoln follows the moth to another section, where he discovers the "lottery" is actually a disguise to remove inhabitants from the compound, where the "winner" is then used for organ harvesting, surrogate motherhood, and other purposes for each one's sponsor, who is identical to them in appearance.
Merrick learns Lincoln has discovered the truth, which forces Lincoln to escape. Meanwhile, Jordan has been selected for the island. Lincoln and Jordan escape the facility, where they emerge in an Arizona desert. Lincoln explains the truth to her, and they set out to discover the real world. Merrick hires Burkinabé mercenary and former GIGN operative Albert Laurent to find and return them unharmed to the compound.
Lincoln and Jordan find McCord, who explains that all the facility residents are clones of wealthy and/or desperate sponsors, who are kept ignorant about the real world and conditioned to never question their environment or history. McCord provides the name of Lincoln's sponsor in Los Angeles, and helps them to the Yucca maglev station, before mercenaries kill him. In New York, Jordan's sponsor, model Sarah Jordan, is comatose following a car crash and requires transplants from Jordan to survive. Lincoln's sponsor, Tom Lincoln, gives Lincoln some explanation about the cloning institute, causing Lincoln to realise that he has gained Tom's memories. Tom agrees to help Lincoln and Jordan but secretly contacts Merrick, who sends Laurent and the mercenaries to their location. Lincoln tricks Laurent into shooting Tom, allowing him to assume Tom's identity.
Merrick surmises that a cloning defect was responsible for Lincoln's memories and behavior, resulting in him and every future clone generation to question their environment and even tap into their sponsor's memories. To prevent this, he decides to eliminate the four newest generations of clones. Lincoln and Jordan, however, plan to liberate their fellow clones. Posing as Tom, Lincoln returns to the compound (allegedly to have a new clone created) to destroy the holographic projectors that conceal the outside world. Jordan allows herself to be caught to assist Lincoln's plan. Laurent, who has moral qualms about the clones' treatment after witnessing their fight for survival and learning that Sarah Jordan may not survive even with the organ transplants, helps Jordan. Lincoln kills Merrick and the clones are freed, seeing the outside world for the first time. Lincoln and Jordan sail away in a boat together.
The film was nominated for three Teen Choice awards.
The film was the subject of a lawsuit due to similarities with the 1979 film; Clonus.