John Greene’s novel combines elements of a mystery, love story, and hero’s quest. The protagonist, Quentin Jacobsen (known as Q), sets out on a quest to find his beloved old friend, Margo Spiegelman. Nourishing an unrequited love for her since childhood, initially the teenage boy is concerned about Margo’s increasingly volatile behavior, including pranks that have become criminal acts. When she disappears, however, he and some other friends go looking for her.

Paper Towns is also a coming-of-age story, in that Quentin must come to terms with his idealistic, romantic, and gender-biased worldview. When located, far from being relieved at being found, Margo lambasts Quentin for his antiquated ideas about male-female relations: he has been living a fantasy in which men are knights who rescue damsels. As it seems he will adjust positively to this change, the reader can see that Quentin has grown through the experience despite its unanticipated outcome.

Paper Towns is a deconstruction of the "manic pixie dream girl" trope. Margo Roth Spiegelman, the leading lady of the novel, is an adventurer who seems perfect and wild in every way. Very few people know anything about her. The narrator of the novel, Quentin, believes that Margo is a "miracle" and spends most of the book viewing her as an answer to his problems rather than as a person. The book is about Margo's disappearance and Quentin's determination to find her, but more than that, it's about Quentin and Margo both finding themselves. The original setup looks like Quentin is going to find Margo and "get the girl," but at the end it turns out he knows just as little about Margo as Margo knows about herself. He realizes that he's been disingenuous about Margo's personality by viewing her as more of an idea than a person, and also realizes that he has to let Margo live her own life and be a real person.

John Green has stated that his purpose in writing Paper Towns was to rectify something he had not accomplished in Looking For Alaska—creating a troubled female character who stood on her own rather than being a plot device for his narrator's development.