Loss, tragedy, and suffering
Daniel starts this novel in a state of innocence, but he ends the novel fully aware of the trauma and tragedy that life often contains. In the novel, that happens indirectly—he learns about the worst parts of life by empathizing with his literary idol, Julian Carax. Through understanding Carax's life, Daniel sees the truth about life, the beauty of love, the tragic fate of man, the universal nature of extreme suffering—all of it. That means that Daniel has a choice. In light of this new knowledge, his choice to accept Beatriz and to commit himself to her with true commitment, it's done knowingly. He understands the cost, but he still says, based on the beauty of Carax's literature, the love he shared with Penelope must have been worth the horror. He accepts his fate, so he accepts tragedy.
Deceit and malevolence
When Julian finds out that his true love has died, it turns out to have been the result of two deadly forces: Deceit and malevolence. Because Julian and Penelope's parents were deceitful with them (never disclosing that they were having an affair with each other), they hold Penelope to a standard they never even explain to her—not even after the fact. They refuse to explain themselves, because their motives are indefensible. The reason that the parents don't make use of honesty is because they are being motivated by malevolence. The truth of the matter is that the parents who refuse to help Penelope are hateful. They let her die, and her baby. In the context of Daniel's story, this is the painful truth behind Coubert's burning books—Carax never healed from the trauma of that malevolence.
The meaning of life, and family love
At the end of the novel, Daniel has completed his journey, so to speak. With new awareness about life, he has to make a choice about commitment. By submitting himself to love, he gains a reward—Beatriz's love and affection. But he also accepts the cost. He accepts the implicit cost of vulnerability for instance. Why? Because he has learned this thematic lesson: That ultimately, the meaning he found in his favorite book was the same meaning he would eventually discover in his own life through commitment.
