The story is set in the country of Opium, a wide strip of land between Aztlán (now called Mexico), and the United States. It was created at some time in the past from portions of both countries, including at least the American states of Arizona and New Mexico. Opium is ruled by Matteo Alacrán, also known as El Patrón. The country consists of several drug-producing Farms, of which the Alacrán estate (which produces opium poppies) is the largest. El Patrón's work-force consists of "eejits", humans with computer chips implanted in their brains that render them unable to complete more than simple tasks. These "eejits" act, or cease to act, only when ordered to do so. Depending on the nature of the task, an eejit will continue performing this task until they die, unless told to stop by an overseer. Most of the eejits in El Patrón's control were once illegal immigrants enslaved by the Farm Patrol after being caught crossing the border of Opium from the United States or Aztlán. The Farm Patrol are a border patrol force of ex-convicts from other countries tempted to work for El Patrón with the offer of protection from the police and judicial system of their home nations.
The main character, Matt, is a clone of El Patrón, an incredibly powerful drug lord who is over 140 years old. El Patrón created eight previous clones, raised as Matt was, for the purpose of organ transplants for El Patrón to survive long after his own have shut down due to age. Matt and the other clones were grown from skin cells taken from El Patrón decades ago and frozen until needed for a new clone. These cells were cultured as stem cells in a test tube, then transferred into a breeding cow to gestate when it became clear that they were going to survive. For the first six years of his life, he lives in a small house on the edge of the poppy fields with Celia, a cook working in El Patrón's mansion. One day, he is discovered by two children (Emilia and Steven). The next day they return, and bring Emilia's sister, María, who immediately captivates Matt. They observe him through the living room window of Celia's house for a while, but soon become bored and turn to leave. Matt is so overcome by longing for other children his age and worry that María will be eaten by a mythical creature that he smashes the window and jumps out to save her. Never having experienced pain before, he was unaware of the danger in jumping barefoot onto smashed glass. The children carry him to El Patrón's mansion to be treated for his injuries. The people there treat Matt kindly until Mr. Alacrán, El Patrón's great-grandson, recognizes him as a clone.
For the next few months, he is treated as an animal by most of the Alacráns, and is locked into a room filled with sawdust for his "litter". The inhabitants of the Big House, meanwhile, are so disgusted by him that they all move to different wings of the mansion, as if afraid of contamination. However, María discovers where he is being kept and informs Celia, who tells El Patrón about Matt's filthy conditions and abusive treatment. El Patrón immediately punishes the maid, Rosa, who was in charge of Matt, gives Matt clothes and his own room, and commands everyone to treat him with respect. It is later discovered that Rosa's punishment was to become an eejit in charge of horses in the Big House's stable. Matt is also given a bodyguard, named Tam Lin, a reformed terrorist who becomes a father figure to him. Still, everyone but Celia, María, and Tam Lin look upon Matt with ill-disguised revulsion, only hiding it when El Patrón is around.
Matt lives in the Big House for the next seven years. He and María quickly become friends, and friendship gradually blossoms into romance. However, Matt is deliberately kept in the dark by everyone about his identity and purpose until a cruel joke reveals to him that he is a clone. Matt also discovers that all clones are supposed to be injected when "harvested" (born) with a compound that cripples their brains and turns them into little more than thrashing, drooling animals. From then on, he studies and learns the piano with a vengeance, in a state of denial. In his heart, Matt already knows the reason for his existence, yet he convinces himself that El Patrón would not hire tutors for him and go to all the trouble of keeping him entertained if he were intending to kill Matt in the end, and that El Patrón must want Matt to run the country when El Patrón dies.
At Steven and Emilia's wedding, El Patrón has a near-fatal heart attack. Matt and María, who have by this time realized they love each other, attempt to flee in the ensuing chaos but are betrayed by Steven and Emilia. María is taken back to the convent where she studies, and Matt is taken to the Big House's hospital, where El Patrón at last confirms that Matt was created only for the purpose of organ donation to keep El Patrón alive. At that moment, Celia reveals that she has been giving Matt carefully measured doses of arsenic, which, though not large enough to kill Matt, would certainly be fatal to one as frail as El Patrón; El Patrón becomes so enraged that he has another heart attack that is fatal at last. Mr. Alacrán orders Tam Lin to dispose of Matt; Tam Lin pretends to comply, and ties him to a horse and rides away apparently to dispose of him. But instead, he gives Matt supplies and sets him on a path to Aztlán.
Arriving in Aztlán, Matt comes across a kind of penal colony for orphans. These orphans are called the "Lost Boys", and Matt is sent to live with them by a group of men known as the "Keepers," who are fervent followers of Marxism. The Keepers operate plankton farms, forcing the orphans to do manual labor and subsist on plankton. The Keepers enjoy luxurious quarters and delectable food, claiming that this is fair because they "earned" the right to do so by working hard during their childhood.
Matt is at first an outcast because the other boys think he is a spoiled aristocrat. However, Matt becomes a hero when he defies the Keepers and leads the boys in a rebellion against them. Matt then flees with his three friends among the Lost Boys. They struggle to the nearest city, San Luis, then go to the convent to find María and her mother, the politically powerful Esperanza Mendoza.
Esperanza thanks the boys for giving her an excuse to charge the Keepers with drug trafficking: for years, many have known about it, but no one has had sufficient evidence for a search warrant. Matt also learns that Opium is in country-wide lockdown. He manages to re-enter the country, but only to learn that the entire Alacrán family is dead, and the estate is empty except for numerous servants including Celia, Daft Donald, and Mr. Ortega. Tam Lin and everyone at El Patrón's wake drank poisoned wine that El Patrón saved to be served at his funeral. Tam Lin knew that this wine had been tainted, and decides to drink it anyway, as penance for accidentally killing twenty schoolchildren in an ill-fated bombing many years prior. El Patrón wanted to either run the business forever, or have it and everyone else die with him. Matt, being the new El Patrón, will become the new ruler of Opium but he plans to dismantle the regime.