In the futuristic country of Opium, a scientist grows a clone from the cells of the powerful drug lord, Matteo “El Patrón” Alacrán. The clone, known as Matt, spends the first six years of his life hidden away inside a house in a poppy field with his beloved caretaker, Celia. Matt’s small, safe world suddenly expands when he is discovered by three children, Steven, Emilia, and María, who bring him to a large mansion beyond the fields. A man named Mr. Alacrán appears at the mansion and becomes enraged and disgusted with Matt. Suddenly, Matt is locked in a room with the cruel maid, Rosa, and the cold doctor, Willum, supervising him. Matt lives in filth there, until Celia and María rescue him. Matt meets El Patrón, the owner of the mansion and the head of the Alacrán family. Matt and El Patrón immediately get along, and El Patrón declares that Matt shall receive an education and no one shall ever hurt him.
Matt lives inside the mansion with Celia and Tam Lin, his bodyguard. Tam Lin shows Matt the oasis just beyond the estate and teaches him outdoors skills. He also speaks with Matt about the ability to mold one’s own personality by choosing to do what is moral and kind. He also tells Matt about the eejits, people with computer chips implanted in their brains so they can do nothing but follow simple orders. All the other servants and family members, except for the kind María and the wicked Tom, ignore Matt. Matt is not sure why, but he begins to realize everyone’s dislike of him has something to do with him being a clone.
Matt excels at academics and learns to play beautiful music. He hopes one day his accomplishments will change society’s perception of him despite his status as a clone. At El Patrón’s birthday party, Matt demands that María kiss him in front of all the guests to show he deserves to be treated better than an animal. María is angry at his cruelty toward her. Later, Tom tricks Matt and María into seeing another clone, this one with its brain destroyed. María is horrified and stops speaking to Matt; Matt hides María’s beloved dog so she will have to come find it and talk to him. Somehow, the dog dies, and Matt is blamed. After this incident, both María and Tam Lin leave Matt alone at the mansion.
Matt and María reunite at the funeral of El Viejo, El Patrón’s grandson. They discover Felicia, Tom’s mother, killed María’s dog to blame Matt. María forgives Matt and makes him promise to live a moral life before she leaves again for school. Matt continues to explore the estate and the nature surrounding it. He learns from Farm Patrol agents that Tam Lin is a former terrorist who accidently killed 20 children in a bombing. Late one night, El Patrón has a heart attack and Matt is rushed to the hospital. However, Matt himself becomes suddenly sick and passes out. When he wakes up, El Patrón has survived by receiving a heart transplant.
Matt begins to mature and grow into a man. He reunites with Tam Lin but is confused and angered by both Tam Lin and Celia’s secretive behavior. He begins to contemplate all he has heard about clones in his life, and he realizes that clones in Opium are created for organ transplants. He reasons that El Patrón could not possibly intend to kill him for organs, because El Patrón gave him a quality education and a luxurious life.
The entire Alacrán family comes to the estate for Steven and Emilia’s wedding. El Patrón has another heart attack, and Matt is captured and brought to the hospital to donate his heart to El Patrón, despite María’s attempts to help him escape. Celia reveals that she has been feeding Matt poison so he cannot donate organs. El Patrón dies. Mr. Alacrán orders Tam Lin to kill Matt, but instead Tam Lin helps Matt escape over the mountains in the country of Aztlán.
In Aztlán, Matt comes under the custody of the Keepers, men who are in charge of the Lost Boys, the orphans of people arrested by Farm Patrol while crossing the border into Opium. The Keepers enforce a hypocritical, collectivist regime, so Matt escapes with the Lost Boys Chacho, Fidelito, and Ton-Ton. They find María and her activist mother, Esperanza, in the convent where María goes to school. Esperanza tells Matt that Opium has been on lockdown since El Patrón’s death and only El Patrón’s DNA can override the security system. She tells Matt that not only must he be the one to open up Opium again, he is the rightful leader of Opium because he is the genetic copy of El Patrón.
Matt returns to Opium, planning on assuming leadership and undoing the crimes El Patrón committed. He finds out that only Celia and a few other servants are still alive. Before his death, El Patrón set aside a bottle of special wine for all his family and servants to drink at his funeral. He poisoned the wine, so that everyone died and Opium could not go on after his death. Tam Lin knew of this plan but drank the wine anyway, in order to atone for his crime of killing the schoolchildren. Matt is angry at Tam Lin for abandoning him and he does not know how he will begin the difficult work of undoing the injustices of El Patrón. However, he knows he still as friends, like María, Celia, and the Lost Boys, to help him.