Rhetoric as magic power
The novel suggests quite clearly that the real reason for the school is to train children to become brilliant rhetors. The nation is at war in wars they call "The Persuasion Wars," and Emily is asked to grow into a powerful voice to join the battle. The act of rhetoric and persuasion is likened to a magic power, as if she is part of the X-Men, but her only super power is convincing argument. This power is magical in a way, because after all, language is quite mysterious, and by saying the right thing at the right time, people can radically alter human history.
Isolation and suffering
The lives of the two protagonists are difficult for two reasons. They are lonely, and they are suffering. Either one of those problems would have been unpleasant, but without someone to share pain and frustration with, they are asked to endure it alone. For Emily, the theme grows, because she wants to be in love, but the school doesn't allow her to do so. They treat her as a military weapon, more or less, ignoring her deep pains and struggles as a lonely orphan.
Passion and art
The novel brings the themes of suffering and loneliness full circle to art and passion. The school encourages Emily to explore her ability to express meaning through words, which is an art form. For her, it is also a passion, and these two are intertwined throughout the book. For instance, the leadership of Emily's covert school are named after famous poets who wrote about passion and suffering.
