2044. Climate change and a series of solar storms have turned the surface of the planet into a desert and killed 99.7 % of Earth's population, leaving only 21 million people alive around the world, living in a single city covered by mechanical clouds to make rain. Trying to rebuild the world again, a robot company named ROC Corporation create Automata Pilgrim 7000 with two security protocols: 1st, a robot cannot harm human beings, and 2nd, a robot cannot alter itself or another robot. But this situation changes when police officer Sean Wallace shoots and destroys a robot that appears to be altering itself. With the company worried by the possible implications if the case were made public, insurance agent Jacq Vaucan is chosen to investigate. Vaucan tries to convince his boss, friend and brother-in-law Robert Bold to transfer him and his pregnant wife Rachel to the coast, with Bold accepting the request if Vaucan solves the case. Going with Wallace to a brothel, they meets a robot in blue wig named Cleo, who is shot by Wallace in the belief that Cleo will go with the mysterious repairman that Vaucan calls The Clocksmith. However, Cleo travels to a mechanical workshop run by Dr. Susan Dupré, who informs Vaucan about a terrible possibility: that the robots can alter their second protocol themselves to acquire self awareness, implying a non-human intelligence that could surpass the human brain. Vaucan informs Bold about this, but ROC's chairman intercepts the message. When Dr. Dupré is killed in front of Vaucan by ROC's hired assassins, he and Cleo flee the city for the desert. Forced to meet ROC's chairman, Bold is told about the secret of the two protocols: that the Pilgrim 7000's prototype was created without them, and due to its unlimited intelligence and learning, it overcame its human owners just eight days later. All subsequent Pilgrims were then created with the protocols to limit their capacity and control them. Fearing the extinction of the human race if all Pilgrims evolve beyond the protocols, ROC's chairman blames Vaucan for Dupré's assassination and the alteration of the robots as an easy scapegoat. Wallace is hired to find Cleo and Vaucan, and kill them. Vaucan, Cleo and three robots travel across the desert to the forbidden and radioactive zone to meet The Clocksmith. There Vaucan finds himself witness to something that could alter the destiny of all life on Earth.