Barcelona, shortly after the end of the Spanish Civil War; Daniel Sempere is a young boy who is very close to his father. As a special treat, his father takes him to a mysterious place called the Cemetary of Forgotten Books, a secret place that only the initiated are allowed to enter. The Cemetary is a huge library of old, rare titles that are lovingly tended to and preserve by only the select amongst the initiated. Tradition has it that each new initiate is permitted to take one book out of the library, something special of their own choosing; they are to guard it with their life, for the whole of their life. After initiation Daniel selects a book called The Shadow of the Wind by Julian Carax. As soon as he and his father get home he starts reading the book, quickly losing himself in its pages, and becoming completely engrossed. Daniel starts seeking other books by the same author, who is pretty much unknown, but he can't find any. There is another person looking for Carax books as well; Daniel is told about a sinister character who calls himself Lain Coubert, the same name as the character in The Shadow of the Wind who turns out to be the devil. "Coubert" has been looking for Carax's other titles so that he can burn all of them.
Daniel's mission to track down Carax's other books leads him on a tangent and soon he is trying to trace the history of Julian Carax's ancestral family tree, not just his writings. He even gets his friend Ferman involved although he cannot tell him much because the initiates of the Cemetery are not allowed to talk about their association with it. As he gets older, he remains as obsessed with his quest as he was when a young boy. Together, Daniel and Fermin delve more and more deeply into the past, inevitably turning over stones that some would prefer had been left unturned. This alerts Inspector Fumero to their existence and their quest; he is a murderous, emotionless man who threatens their lives.
In searching for the writings of Julian Carax, Daniel and Fermin also unearth a long buried love story. Julian Carax was the son of a milliner, Antoni Fortuny, and his wife Sophie Carax, whose last name Julian preferred to take rather than that of his father. The love of his life was a woman named Penelope Aldaya, daughter of a wealthy Spanish man and his indulged American wife. Julian and Penelope were in a secret relationship for four years, and as they were about to be revealed as lovers, decided to elope to Paris. The plan was for the two of them to meet at a pre-planned spot but Penelope doesn't turn up to meet Julian. Julian stays on in Paris but can never move on with his life; he needs to know what happened to Penelope and why she didn't meet him when he knew that she loved him. He returns to Barcelona, to discover that nobody had heard from Penelope since the day of their elopement. He also learns that he and Penelope are half brother and sister - Julian's mother had an affair with Penelope's father, and after Julian left for Paris, Penelope's parents imprisoned Penelope because they were angry and ashamed of her for having an incestuous relationship - although she had never known that's what it was. Penelope was pregnant with Julian's baby, and during childbirth, she became ill. Despite calling for her parents to help her, they ignored her cries and pleas, letting her die, and burying her in the family crypt next to her stillborn son, Daniel. Julian is bereft, and cannot stand living without her. He changes his name to Lain Coubert and starts burning all of his books.
When Daniel finishes searching for answers about the book he marries his long time love Beatriz Aguilar. When Bea gives birth to their first born son, they name him Julian, in honor of Julian Carax. Daniel's life turns full circle; he takes his son to the Cemetary of Forgotten Books, and shows him The Shadow of the Wind.
