The first part of Lexicon takes place near Arlington, Virginia, but the exact location is not known. That is because a school is located there that must remain top secret, because they teach students to have extraordinary powers. The art of persuasion through language has been around for many centuries, but a school teaching it is a different story. The people that go here must take rigorous tests before admittance, but, once they are in, they become part of an exclusive club.
Emily Ruff is an orphan, but excels in academic areas in her life. Despite this, her only income living in San Francisco is scamming people off of a card game she plays on the street. One day, a recruiter for the exclusive school sees her, and believes she may be fit for acceptance. Emily accepts his invitation to take a few tests, and is eventually admitted to the school.
Quickly, she is flown across the country. At the school, there are three main men in charge, all of whom have names of famous poets from the past. They take the names of poets because of their art of persuasion. Their names are Bronte, Eliot, and Lowell. Each of them constantly tells Emily that secrecy is very important, and everything in her life will be ruined if she reveals information about the school to the public. Who knows what would have happened if she had failed the entrance exams...
After a while, it is evident that Emily is very talented in what she does, and she becomes the most skilled pupil in her class. Still, she is human, and falls into her own emotions sometimes. According to the school, it isn't allowed, but, nevertheless, Emily falls in love.
Another aspect of the story is told about the character Wil Jamieson. One day, he is caught in a fight with two men in an airport bathroom, and he truthfully has no idea why. Although Wil does not attend the secret school, he has become in a mess that he doesn't even know about yet.
Eventually, Wil travels to Broken Hill, Australia, a town that was decimated by war. It is explained to him that the whole world will look like this if he does not cooperate, but he still doesn't know what is going on. Persuasion wars continue to occur throughout the novel, with the number of deaths rising very high.