Matt Alacrán is a clone living in Opium, a small country between Aztlán, formerly known as Mexico, and the United States. The intelligence of most clones is destroyed, but because of the wishes of his powerful original, Matteo Alacrán (El Patrón), Matt's intelligence is left intact.
For the first six years of Matt's life, he lives alone with Celia, one of El Patrón's cooks, in a hut on the edge of El Patrón's expansive opium ranch. Matt's only experience of life beyond the hut comes through TV and books; stuffed animals are his only friends. Once a month, a doctor visits.
When Matt is 6, three children discover Matt in the locked hut. He is too surprised and afraid to speak to them. The three children, Steven Alacrán and Emilia and María Mendoza return the next day. Matt breaks a window to get to them, but he is badly cut by shards of glass and passes out. Steven carries him to El Patrón's house, where a servant removes the glass. A tattoo on Matt's foot reveals that he is the property of the Alacrán Estate. Steven's father enters, recognizes Matt as El Patrón's clone, and has Matt thrown onto the lawn.
A servant takes Matt to a back part of the house for medical care. Celia isn't allowed to see him, and he isn't given any food. Later, María sneaks food to Matt. They share stories, and she sleeps in his room. As a result, María is sent away.
The doctor and the servant continue to attend to Matt, but Matt refuses to talk to them. After his wounds heal, the servant removes his bed and fills his room with sawdust like a chicken coop. Steven's brother, Tom, regularly taunts Matt through the window. Six months later, Matt hits Tom in the face with a rotten orange that he kept hidden under the sawdust. María returns and brings Celia with her. Celia promises to get Matt out.
Not long afterward, Matt is washed up and taken to El Patrón. The doctor diagnoses Matt as malnourished and allergic to the chicken litter. The doctor denies any prior knowledge to El Patrón. Matt likes El Patrón, who calls him mi vida, "my life," feeds him rich foods and tells him stories. El Patrón insists that Matt be well cared for and educated. His bodyguard is Tam Lin.
Matt begins hiding to watch Felicia, Steven and Tom's mother play piano in the afternoons and discovers a secret passageway in a closet. While spying from the passageway, Matt learns that Felicia is a laudanum (tincture of opium) addict.
Felicia tells Matt that María wants to meet him at the Alacrán hospital on the ranch. Then María, Tom and Matt hear mewing. Tom leads them to see a clone strapped to a bed. It mews and screams and writhes in its restraints. Matt says it needs to be rescued. María disagrees and leaves with Tom.
Matt goes to Celia and cries. Celia explains that the clone at the hospital had its brain destroyed by an injection. Matt decides to explain this to María but can't talk to her. He snatches her dog and leaves a note for María to meet him and says he'll return her dog. When he goes to meet her, he learns that the dog is dead (Felicia had killed it). Maria's father tells Matt that he won't be allowed to see María again because he allegedly killed her dog. He denies the accusation, but even Tam Lin doesn't believe him. Tom, Tam Lin and María all leave the ranch.
Three years later, Matt finds a blanket, a stash of water and a metal chest. The chest contains supplies and a letter from Tam Lin explaining that he had not wanted to leave and that Matt might need the supplies.
Matt must attend the funeral of El Patrón's grandson. María is at the funeral holding hands with Tom. Tam Lin is there with El Patrón. The priest rages that Matt is in church. María defends Matt and leads him away to the music room in the main house. When they hear people coming, Matt leads her to the secret passage.
From the passage, they find a room where they can talk uninterrupted. María explains that she forgave Matt for killing her dog. He is so happy to see her and talk to her again that he doesn't defend himself. He comments about the priest's reaction to him. María explains that Matt is soulless because he is a clone. They hear voices and return to the secret passage. Tom and Felicia enter the room. They are looking for Matt and María using the security computers in the room. Felicia tells Tom how she killed María's dog. María apologizes to Matt for accusing him. Tam Lin finds them in the passage and rushes María away.
Matt is 14 when he learns that most clones are used for extra body parts for transplants. María meets Matt in the passageway and confides that she is to marry Tom. As the wedding is starting, El Patrón collapses. He is rushed to the hospital.
Matt concludes that El Patrón wants Matt’s healthy heart. María confirms Matt's suspicions. She plans to escape with him in her hovercraft after dark. They exit using a secret pass to the hovercraft launch pad that only El Patrón and Matt can safely activate with their DNA. At the hovercraft, Emilia and Steven stop them, and Matt is taken to the hospital.
At the hospital, Matt is strapped to the table, tested and brought to El Patrón. Celia announces that Matt's heart can't be transplanted because she has been poisoning him with arsenic since El Patrón's first heart attack. This enrages the weak El Patrón so he is rushed out of the room. A strand of Matt's hair is tested to confirm he has been poisoned.
Hours later, Steven's father and Tam Lin return to inform Matt that he will be euthanized. El Patrón is dead. Matt is informed that Celia will be made into an eejit for poisoning him. An eejit is a person whose executive brain functions are eliminated by a computer that is implanted directly into her brain.
Tam Lin tells Matt that he cut Celia's forehead as though she had an implant, without giving her one. Then, he tells Matt to escape to Aztlán and pretend to be an orphan at the border. He is then to find María at her school in San Luis.
The way to Aztlán is difficult. Matt is picked up by Keepers, guardians of orphans, who plan to send him to San Luis to work in a plankton factory. He is locked up with other orphan boys: Fidelito, Chacho and Ton-Ton. A Keeper, Jorge, leads all the boys in a verbal attack against Matt because he failed to confess any "sins."
Later, Chacho and Matt explore beyond the fence and discover a whale boneyard. That night, Matt refuses to confess again, so Jorge canes an innocent Ton-Ton. Matt still refuses and accuses Jorge of wanting him to be a zombie. Fidelito confesses for Matt, so Jorge intends to beat him, but Matt speaks up and takes the beating.
While he and Ton-Ton are in the infirmary with their injuries, Matt learns that the Keepers take laudanum each night and that San Luis is a few miles to the north. He develops a plan of escape.
That night, Jorge decides to cane Fidelito when Matt doesn't confess properly. When Jorge lunges at Fidelito with the cane, Matt stops Jorge. The other boys attack, too, but are stopped by more Keepers. Jorge blames Matt as the leader.
As punishment, Matt and Chacho are thrown into the boneyard. Their hands and feet are taped and they sink deep into the bones. Matt cuts his feet free on a sharp bone. He is energized by rainwater from a storm and is able to wiggle through the bones and climb out. He hears Chacho snoring, submersed in the bones. Chacho is unconscious, possibly from shock or other injuries sustained by falling into the bone yard.
Meanwhile, the orphans pen the Keepers in their compound, and Ton-Ton gives them extra laudanum to make them sleep into the next day so several boys can escape. Ton-Ton and Fidelito escape and bring a shrimp harvester with a mechanical claw to clear away the bones that cover Chacho. When Chacho is revived, all four boys ride the shrimp harvester toward San Luis. They continue to plod along on the solar powered harvester until nightfall. Chacho has trouble breathing. Matt and Fidelito continue on foot to find a doctor.
As Fidelito and Matt walk, Matt has an asthma attack. Fidelito finds an older couple who gives Matt an inhaler and sends an ambulance for Chacho. The old man takes Fidelito and Matt to Chacho, who is in the hospital at the convent where María goes to school.
Ton-Ton and Fidelito stay at the convent to attend boarding school. As Matt recovers, María visits him. María and her mother inform Matt that the country of Opium is in lockdown. They want him to go back because El Patrón's DNA signature overrides the lockdown. María's mother informs Matt that according to international law, he isn't a clone if the original Matteo Alacrán has died. He is now El Patrón.
Matt takes a hovercraft back to Opium. He has no trouble breeching the lockdown and entering the ranch house. Celia enters and tells him that everyone who drank special wine left by El Patrón died at his wake, including Tam Lin, Emilia and Steven; everyone except the staff and the eejits. Matt starts making plans to break down the empire.