We first meet Clay Jannon, the protagonist and narrator of Mr. Penumbra’s 24-Hour Bookstore, shortly after he has lost his first job as a web designer for NewBagel, a casualty of the recession that is sweeping America. When he spots a help-wanted sign in the window of a bookstore, he embarks not only on a new career but also on a journey that will see him attempt to decipher a centuries-old encrypted manuscript. While he is grateful for his job as a night clerk at the book store, he can’t help but feel bored; despite his best efforts to attract business with an online marketing campaign, the store is largely bereft of customers. The campaign is not a total failure, however, as it lures Kat Potente into the store with the promise of a coupon. Kat doesn’t buy a book but she and Clay do embark on a romantic relationship. What few customers the store does have are very strange and solitary individuals, whose visits and behavior Clay is required to record in the store’s logbook. These customers all borrow books from the tall shelves at the back of the store that Clay thinks of as the Waybacklist and he wonders if they are all part of an obscure book club. His curiosity about this club grows and, along with his friend Mat, he discovers that all the books on the Waybacklist are written in code. At the same time, to keep himself occupied and inspired by the anonymous hacker Grumble, Clay has been building a 3-D model of the bookstore on his laptop. This model will lead him to another important discovery about the bookstore: the Founder’s Puzzle. Uploading the store’s database of books and information from a recent logbook to his computer model, Clay can track the borrowing patterns of the Waybacklist club. He is startled to discover the image of a face hidden in the store’s shelves and when he shows Mr. Penumbra what he has found, his employer is both delighted and angry.

Clay’s discovery prompts Penumbra to leave the store, leaving Clay unsure whether he still has a job and intrigued as to who the “Founder” is and what it all means. In order to find out more, he questions one of the Waybacklist customers, Rosemary Lapin, and learns that the ancient organization she and Penumbra are part of—the Unbroken Spine—are involved in deciphering encrypted books. Another member of the fellowship Tyndall reports that Penumbra has been summoned to the organization’s library for punishment. Clay is overcome with guilt and later, having broken into Penumbra’s office, he learns that Penumbra is heading for New York and, along with Kat and his friend Neel, Clay is determined to follow him there. Drawing on Kat’s technical know-how, the small group manages to find the location of the Unbroken Spine’s secret library and stake it out, waiting for Penumbra to arrive. Penumbra reassures them that everything is under control: he has a plan but needs their help. He tells them that the Unbroken Spine is an organization dedicated to decoding a book written by a fifteenth-century Venetian printer, Aldus Manutius, a book they believe can reveal the secret to immortality. Penumbra, inspired by the fact that Clay solved the founder’s Puzzle so quickly using computers, wants to apply similar techniques to Manutius’s book. However, the leader of the Unbroken Spine, Corvina, is a traditionalist and won’t allow it. To overcome this obstacle, Penumbra proposes that they break into the library and make a digital copy of the book so that they can try new methods in secret. Clay and his friends agree and make the necessary preparations.

Clay successfully scans Manutius’s book and on their return to San Francisco, Kat arranges for them to have access to some of Google’s resources to try and crack the code. Unfortunately, this attempt is not successful and Penumbra once again disappears. Clay is still determined to find him and asks Deckle, another member of the Unbroken Spine and Penumbra’s friend, for help. Deckle agrees on the condition that Clay retrieve an item that had been stolen from the fellowship years before: the Gerritszoon punches. Griffo Gerritszoon was a friend of Manutius and developed the Gerritszoon typeface, still widely in use today; the punches are the original molds the fellowship uses to create letters with which to print their books. Clay agrees to this deal and with help from his friends manages to locate the lost item. Before he can tell anyone, Clay has a revelation while listening to the audio version of his favorite books—The Dragon-Song Chronicles—whose author, Clark Moffat, he had recently discovered had been a member of the Unbroken Spine. He calls a meeting of all those concerned and reveals to them the deciphered text of Manutius’s book. The key to the book was hidden in the Gerritszoon typeface, something which Moffat learned and wrote into his books. Furthermore, Clay reveals that Manutius’s text does not holds the secret to eternal life, rather, it is a simple memoir. Corvina is disgusted and leaves when Clay announces this but Penumbra is delighted that the mystery has been solved. Together, he and Clay start a new business that tackles problems at the intersection of books and technology: they call it Penumbra.