Clay Jannon tells of his recent firing from his job as a web designer in the 2000's recession. When he loses his deal with NewBagel, he finds a job as a clerk at a book store. The job makes him happy, but occasionally, he gets bored in the evenings. He manages to stir up some business with his online marketing, but regardless, the store feels the full weight of the recession.
The marketing efforts do allow Clay to meet a new customer, Kat Potente, and the two hit it off. Each customer who enters the store is recorded by Clay who also jots down their behavior. The strangest customers are those who borrow books from the Waybacklist, a made up name Clay gave to the back wall of books. When he checks it out with his friend Mat, they discover that the entire Waybacklist is written in a cypher, and they begin trying to decode its messages.
Clay gets bored and makes a 3D model of the store, and upon seeing its architectural layout, discovers the Founder's Puzzle. There are paintings of faces behind the books on the shelves. When Clay tells his new boss about all of his findings, the man is confused and bemused, but also curious and interested.
Penumbra leaves in a huff, and Clay asks one of the regulars what she knows. The woman, Rosemary Lapin, tells Clay that they are in an ancient secret society called the Unbroken Spine. When Clay breaks into the back office one night, he discovers that some of the Unbroken Spine are leaving to New York. Clay, Kat, and Neel, a friend of Clay's, follow him to New York.
They confront him and Penumbra confides in the youngsters that they are decoding Aldus Manutius's manuscripts that are alleged to give immortal life. Clay says he can easily decipher the code with computers, but Corvina, the society's leader, has explicitly forbidden the use of technology. Penumbra decides it's worth it, though, so they plan to make a digital copy of the book.
Back in San Francisco, after a successful heist, they work with Google to crack the code. Penumbra disappears again when the plan yields no results. Clay invites Deckle (a society member) to help search for Penumbra, but Deckle will only help if Clay helps him get the "Gerritszoon punches." These refer to the original font plates for Gerritszoon's typeface.
They successfully decipher Manutius's book and discover it is a memoir, not a mystic document. The society disbands with diverse opinions. Penumbra and Clay start a company to help decipher books with computers, named Penumbra.
