Web-designer Clay Jannon has landed a new job working the night shift at Mr. Penumbra's 24-Hour Bookstore. But after just a few days on the job, Clay begins to realize that this store is very curious. There are only a few customers, but they come in repeatedly and never seem to actually buy anything, instead "checking out" impossibly obscure books from strange corners of the store, all according to some elaborate, long-standing arrangement with the Mr. Penumbra. Clay concludes that the store must be in some other secret business. Soon he and his friends embark on an adventure to figure out just what's really going on. But, it turns out the secrets extend far outside the walls of the bookstore.