Percy Jackson experiences several conflicts at the start of the story before he begins his quest to find Zeus's master bolt. In the first chapter, Percy describes his academic challenges and says that he has been diagnosed with attention deficit–hyperactivity disorder and dyslexia. These disorders make it difficult for him to focus in school and succeed academically. Although Percy tries his best to overcome his disorders, he cannot prevent being expelled from several schools.

On Percy's field trip to the museum, his math teacher, Mrs. Dobbs, reveals herself as a Fury and attacks him. Mr. Brunner throws Percy a pen, which turns into a sword, and he vaporizes Mrs. Dobbs. Following the incident, Mr. Brunner and Grover and refuse to acknowledge Mrs. Dobbs's existence. Later on, Percy eavesdrops on Mr. Brunner and Grover speaking about the incident, and Percy feels like he cannot trust his best friend, who is apparently hiding something. Percy responds to this challenge by remaining aloof and leaving Grover behind to visit his mother.

The most significant challenge that Percy faces at the beginning of the story is surviving a Minotaur attack and dealing with the loss of his mother. Percy is not able to save his mother but manages to kill the monster by stabbing it with its broken horn. Once Percy arrives at Camp Half-Blood, he finds it challenging to accept the truth about his identity and the reality that Greek gods exist. He also comes into conflict with Clarisse, who is one of Ares's children. Percy responds by embracing his identity and defending himself against Clarisse and the members of her cabin.