The story takes place in the country of Opium, a strip of land between Mexico (now called Aztlán), and the United States. Opium, which is essentially an opium-producing estate, is ruled by Matteo Alacrán, also known as El Patrón. El Patrón's work-force consists of illegal immigrants whom the Farm Patrol (ex-criminals who are tempted with the offer of protection from the police) enslave when they catch them crossing the border in either direction. These illegal immigrants become "eejits", humans with computer chips implanted in their brains, making them more or less zombies who can perform only simple tasks.

The main character, Matt, is a clone of El Patrón, an incredibly powerful, 140-some-years-old drug lord who intends to take Matt's organs when his own organs fail. Matt was grown from a set of cells that were taken from El Patrón decades ago, then frozen. He was cultured in a test tube, then transferred into a surrogate mother (a cow) when it became clear that he was going to survive. For the first six years of his life, he lived with Celia, a cook who worked in El Patrón's mansion. Though he was told from very young that Celia was not his biological mother, she is his mother figure. 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 window for a while, but soon get bored and turn to leave. Matt is so desperately lonely that he smashes the window and jumps out to follow them. 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, also known as the Big House, to be treated. Though the people there act kindly towards Matt at first, a man passing by (Mr. Alacrán) 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 have all moved to different wings of the mansion, as if they were afraid of contamination. However, María discovers where he is being kept, and informs Celia, who then passes the description of Matt's filthy conditions and abusive treatment on to El Patrón. El Patrón immediately punishes the maid who was in charge of Matt, gives Matt clothes and his own room, and commands everyone to treat Matt with respect. Matt is also given a bodyguard, Tam Lin, who becomes a father figure to him. Still, everyone but Celia, María, and Tam Lin look upon Matt with ill-disguised repulsion, only now they hide it when El Patrón is around.

Matt lives in the Big House for the next seven years. He and María quickly become friends, then more than friends. 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" with a compound that cripples their brains and turns them into little more than thrashing, drooling animals. From then on, he studies and practices 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 him tutors and go to all the trouble of keeping Matt entertained if he was intending to kill Matt in the end, and that El Patrón must want Matt to run the country once he was dead.

Alas, Matt's worst fears are realized: 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 away, and Matt is walked over to the Big House's hospital, where El Patrón at last confirms that Matt lived only to keep himself, El Patrón, alive in the end. 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 mad with rage that he has another heart attack and dies. Mr. Alacrán orders Tam Lin to dispose of Matt; Tam Lin pretends to comply, and ties him to a horse and rides away 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 the 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 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.

Esperanza thanks the boys for giving her an excuse to charge the Keepers with drug trafficking: for years, everybody had known about it, but no one had sufficient evidence for a search warrant. Matt also learns that Opium is in lockdown. No one can enter or leave the country, and there has been no communication. All planes are shot down by automated defense systems, but, Esperanza reveals, El Patrón's DNA signature is overriding, since he is essentially the dictator of Opium.

Matt, who has exactly the same DNA as El Patrón, manages to re-enter Opium, but only to learn that almost no one he knew is still alive. El Patrón has died and he has caused his subjects and possessions to be buried with him. Matt, who is El Patron's genetic heir, becomes the new ruler of Opium.

(From http://en.wikipedia.org/wiki/The_House_of_the_Scorpion, Friday, March 4th, 2011, 3:04 AM)