Several themes can be drawn out of the novel, but the most evident one would read something like "Sometimes one's greatest enemy is oneself." This is obviously the case with Gene, an overly-scholarly, introvert "preppie" who can only exist in terms of showing his superiority over others. In sharp contrast is Phineas, not so studious but well-liked by both students and teachers. Finny's general good will and optimism are flamboyantly shown by the pink shirt he wears along with the school tie uses as a belt. (Finny is so disarming that he even gets away with it!) Despite their deep friendship, the "monster" in Gene comes out for a split second when he intentionally bounces Phineas off-balance on the limb of the tree at the water hole, making him fall.
Several other themes focus on the subject of guilt, confession and forgiveness. Make a statement that best fits your interpretation of the message Knowles is trying to get across. Is it the idea that love can forgive all, or that some acts of violence are irrevocable and their consequences can't be undone? (Remember in the backdrop of what happens at the school between Gene and Phineas, there is a cruel war going on for which the boys are being "prepared.") Along these lines is the idea of the inevitable loss of innocence in one's coming of age.
Critics have sometimes esteemed this book as melodramatic and overly sentimental. Personally, it is one of my favourites; I think it fairly accurately depicts the nature of inner conflict and the difficulty of finding any real resolution or reconciliation with self once one has betrayed a "loved" one.