The House of the Scorpion is a dark, twisted, but ultimately hopeful story about a young clone named Matt who grows up in a dystopian world under the control of a drug lord. Oh, and this drug lord happens to be the man from whom he was cloned. As it turns out, this guy, called El Patrón, cloned our protagonist so that he might harvest Matt's organs to keep himself alive later in life.
Matt's early years are peaceful. He lives in seclusion with his caretaker Celia, who works for the wealthy Alacrán family, of which El Patrón is the head. But when Matt is taken to live in the Big House on the Alacrán estate in the country of Opium, Matt's life takes a dark turn. He faces a never-ending series of hard-knocks: isolation, prejudice, imprisonment, violence, illness, and the threat of death – all before the age of fourteen!
Matt fortunately finds some allies in the mostly mean Alacrán clan: his surrogate mother Celia, his bodyguard-turned-mentor Tam Lin, and his friend-turned-love, María. With the help of these friends, Matt eventually escapes from Opium (and death-by-organ harvesting) and travels to Aztlán, formerly known as Mexico.
After more abuse, hard work, friendships, and near death experiences, Matt finally makes it to safety with María and her mother Esperanza, who is heavily involved in politics and protests in Opium. At the end of the novel, Matt returns to Opium and takes over as the leader of that country, now that El Patrón has died. The novel ends on a fairly optimistic note as the intelligent and idealistic Matt sets out to undo the damage the ruthless El Patrón did during his rule.