Having lost his job as a web developer due to the recession, Clay Jannon finds a new job as the night clerk in the titular bookstore, belonging to the mysterious Mr. Penumbra. Not that he sells all that many books. As well as the normal shelves, with its somewhat eclectic selection of novels and non fiction, there is what Clay calls the “wayback” section of the store, huge shelves of unique volumes, not to be found in any search engine, a sort of strange lending library for the odd individuals who show up with a laminated cards, returning a volume and fetching another at random intervals. Clay is asked to keep a log, describing the appearance of each of the customers and the state of mind each new customer was in when they come to swap a book.
Clay starts using his web developer skills to make a 3D-model of the store and the “wayback” section on his computer, trying to see if there’s any pattern, rhyme or reason to the strange regulars and their lending patterns. He also works on trying to lure new customers to the store, using all the tools available to him in social media to advertise its location. Once he meets Kat, a young lady working at Google, his plans to map the mysterious patterns of Mr. Penumbra’s store really take off, and soon he and his friends are involved in a mysterious quest involving a global conspiracy, a secret organisation, code breaking, data visualisation on a massive scale and possibly the secret to eternal life.