Adventure, mystery, and secrets
The book involves many secrets, including a mysterious ancient society designed to unlock mystic secrets from an encoded book by Manutius. These adventures lead Clay and Kat (along with their friend) to New York, and their decision to involve themselves in the mysteries of Manutius's writings leads to the solution of the code. In the end, they discover that it is not a book of magic at all; it's a personal memoir.
Technology and books
This theme is implicit in the plot (a computer savvy person investigates books during his employment at a book store), but it is also evoked in many other ways. Clay finds secrets by combining his technological savvy with the bookstore. He meets his girlfriend that way, interestingly. He also encourages the Unbroken Spine to take a step into the future, to use computers to decipher the mysterious codes in Manutius's manuscript.
The quest for immortality
One thematic drive of the book is the Unbroken Spine's commitment to discover the secrets of immortality. This theme is coded in metaphors: A group of committed readers is trying to have supernatural experiences with a book. It's a kind of symbolic book club. In other words, the book combines reading with the progress toward eternal life, perhaps to signify that serious readers are having deep, meaningful religious experiences with their books. Interestingly, in the end, when it's decoded, some people wish they had the mystery back.
