2044. The climate change and a series of solar storms have turned in a desert the surface of the planet and annihilated to the 99.7 % of Earth's population, leaving alive 21 million people across the world in a single city covered by mechanical clouds (zeppelins anchored to the city) 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 himself or another robot. But this situation changes when police officer Sean Wallace shoots and destroys a robot claiming that it was altering himself. With the company worried by the possible implications if the case were known by the people, insurance agent Jacq Vaucan is chosen to investigate the happened, while 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 a mechanical workshop property of 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 easily it should overpass the human brain after a test where she mixed a biocore from the Wallace's shot robot with Cleo's own biocore. Vaucan reports secretly Bold about it, but ROC's chairman intercepts the message. When Dr. Dupré is killed in front of Vaucan by a ROC's squad group, he and Cleo run from the assassins, ending outside the city, lost in the white desert that surrounds the city. Forced to meet ROC's chairman, this reports Bold 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, he overcame to its human owners just eight days later. After to escape, all the next Pilgrims were created with the protocols to limit their capacity in order to have them under control. Fearing the extinction of human race if all the Pilgrims evolve beyond the protocols, ROC's chairman blames Vaucan of Dupré's assassination and the alteration of the robots to cover up to the public, and Wallace is hired to find Cleo and Vucan and kill them. According Vaucan, Cleo and three robots more travel across the desert to the forbidden and radioactive zone to meet The Clocksmith, Vaucan will find himself as witness of something that it would change the world as nobody could imagine.