Conflicts come in different forms. The two main categories are internal (character versus self) and external (character versus an outside force).
The main conflicts in this book are external. First of all, there is character vs. technology. Matt’s biggest problem is that he is a clone, and was created through technology instead of the natural way. This leads to the second biggest conflict, character vs. society. Society frowns on clones, and so Matt is hidden until he is 6 years old and then treated like an animal when he is found. Clones aren’t considered people. They refer to him as “it” instead of using “he” like a human. Matt does not really understand the meaning of the word “clone” and does not know why people treat him badly.
There are internal conflicts too, as Matt faces confusion, uncertainty and fear when he learns who he is, and then faces the need to escape.
As the book continues, Matt faces other conflicts. He has a character vs. character conflict with El Patron throughout the book, as well as other characters and The Keepers and others who victimize him.
There isn't only a single conflict in The House of the Scorpion. There are several conflicts that focus on Matt, and each of those conflicts are all related to the fact that Matt is a clone. That's bad because clones aren't considered real people. They are essentially a subgroup of humans. In Matt's case, his entire reason for existing is to be a spare body parts carrier for El Patron. Matt suffers as a clone. He isn't treated well by most people in the book.
The servants went back to ignoring him. The Alacráns treated him like something Furball had coughed up on the carpet.
Additionally, Matt's clone identity is a big internal conflict of his. He knows that he is the exact genetic duplicate of a ruthless dictator and drug lord. Matt fears that he could become exactly like El Patron. Matt struggles to forge his own identity over the course of the novel as well as fearing that being a clone will be his undoing.
He wasn't a clone! He couldn't be! Somehow, somewhere a mistake had been made . . . Was he going to end up strapped to a bed, screaming until he ran out of air?
Eventually, Matt is driven to escape from Opium, and that allows his external conflict with his abusers to essentially end, but his internal clone conflict will always be there. Additionally, the book ends on the hopeful note of Matt returning to Opium as the new ruler; however, that introduces a whole new conflict inside of Matt. What kind of ruler will he be? Will he be able to undo what El Patron has put into place.