The House of Scorpion begins in a dystopian future, on a violence-torn strip of land between the United States and Mexico (known as Opium or “Dreamland”) ruled over by powerful and unnaturally long-lived drug lord El Patron. The protagonist, Matteo “Matt” Alacran, is in actuality a genetic clone of El Patron, and is slated to be harvested for his organs. For the first six years of Matt’s life, he lives with El Patrons’ cook Celia on the edge of the Alacran estate.
One day, he is discovered by three children (Maria, Steven and Emilia) and attempts to escape from them by jumping out of a window, hurting himself badly on the shattered glass. He is then taken to El Patron’s mansion, where his injuries are treated. However, El Patron’s great grandson, Mr. Alacran, realizes Matt is a clone and locks him in a room, where Matt spends several abusive months. Upon discovering this, El Patron is horrified and commands everyone on the estate to henceforth treat Matt with respect, even granting him his own room, bodyguard, and tutors.
For the next several years, Matt lives comfortably in El Patron’s mansion, even befriending Maria and beginning a budding romance with her. He remains blissfully unaware of his true identity and purpose, until an almost offhand joke reveals that he is one of many clones of El Patron. He learns that most clones are injected with something to mentally cripple them at birth, making them little better than drooling animals/organ farms for when the old man’s various ancient organs start to fail. Matt is horrified, but manages to convince himself that El Patron would not have done all the generous things he has for Matt if he were simply planning to slaughter him. He decides that El Patron must be grooming him as a successor for the cartel.
Later, at Steven and Emilia’s wedding, the festivities are thrown into disarray when El Patron suffers a heart attack, meaning that the Matt’s heart (which has been carefully tended) is now required. Matt and Maria attempt to flee the wedding, but are caught by Steven and Emilia. Emilia is whisked away to a convent, and Matt is taken to the hospital and to El Patron, who confirms that Matt was indeed created as an organ donor. Celia then reveals that she has been feeding Matt small doses of arsenic for a long time, which, while relatively harmless to Matt, would likely kill the frail El Patron. The old drug lord flies into a rage at that, suffering a final, fatal, heart attack. Mr. Alacran then orders Matt’s bodyguard (Tam Lin) to dispose of him. Tam Lin pretends to comply, but instead helps Matt escape and sets him on the road to Aztlàn.
When he arrives, Matt encounters a group of orphans known as the Lost Boys, and is sent to live with them by the “Keepers” a group of radical Marxists who operate vast plankton farms staffed by orphans. The children do all the manual labor and subsist on the plankton, while the Keepers live lavishly. Matt is shunned by the other boys, who view him as comparatively privileged, but he quickly becomes their hero upon rebelling against the Keepers and leading the other boys against them in open revolt. Once he has escaped the Keepers, Matt and two friends flee to the nearby city of San Luis, where they encounter Maria and her mother, the politically powerful Esperanza Mendoza. Esperanza thanks them for taking down the Keepers, and Matt learns that Opium has been put on a countrywide lockdown.
When Matt finally manages to renter Opium and make his way to the Alacran estate, he learns that the entire family is dead, having drank poisoned wine at El Patron’s funeral. The cartel leader never planned to die, and decided that in the event he was unable to run the operation indefinitely, he would take everyone down with him. However, Celia still lives, Maria still lives, and Matt decides to take on the role of El Patron in order to truly bring down the cartel.
