In 2019, Lincoln Six Echo and Jordan Two Delta live with others in an isolated compound. This community is governed by a strict set of rules. The residents are told that the outside world has become too contaminated to support life with the exception of a pathogen free island. Each week, one resident gets to leave the compound and live on the island by way of a lottery.
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 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 system to selectively remove inhabitants from the compound, where the "winner" is then used for organ harvesting, surrogate motherhood, and other important purposes for each one's wealthy sponsor, of whom they are identical clones.
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, and emerge in the desert. Lincoln explains the truth to her, and they set out to discover the real world. Merrick hires Burkinab� mercenary and former GIGN operative Albert Laurent to find and return them to the compound.
Lincoln and Jordan find McCord, who explains that all the facility residents are clones of wealthy sponsors, and 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 City, 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 realize 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.