In 2019, Lincoln Six Echo and Jordan Two Delta live with others in an isolated compound. This dystopian 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 so he places probes in Lincoln's body to monitor his cerebral activity. While secretly visiting the 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 pregnancies, and other important purposes for each one's wealthy sponsor, of whom they are clones.
Merrick learns Lincoln has discovered the truth about his existence, which compels Lincoln to escape. Meanwhile, Jordan has been selected for the island. She and Lincoln escape the facility and emerge in the desert. He explains the truth to Jordan, and they set out to discover the real world. Merrick hires Burkinabé mercenary and former GIGN operative Albert Laurent to find and return them to the compound.