One of the conflicts in Paper Towns is the conflict that Quentin feels between being a conventional and what he calls a "well adjusted" (page 6) rule follower on one hand and following what Margo does on the other hand. Even when they are nine and discover a dead body in their neighborhood, Margo wants to investigate, while Quentin wants to go home. When Margo forces Quentin to accompany him on a night of pranks to avenge what some of her friends have done to her, he is an unwilling accomplice. At the end of the book, even though Quentin has deviated from his routine to find Margo, he decides to return to his life rather than accompany Margo on her journey to New York City. In the end, Quentin decides to follow a more conventional life path rather than follow Margo on her uncharted adventures.

Margo, for her part, feels a conflict between what she is supposed to do and what she wants to do. Her conflict arises because she feels ill at ease in society and disconnected from the people around her, and her obsession with paper towns has to do with the superficiality she finds in her friends and family. She first calls Orlando a paper town (page 56), and then she becomes obsessed with finding these towns, which only exist on the map. When these towns appear in encyclopedias or on maps, they are intended to catch people who plagiarize or copy the maps without permission. For Margo, these towns represent the falseness in people she sees around her. Her reaction to this conflict is to continue to run away from home, eventually to a paper town in New York state and then to New York City. She has not necessarily resolved this conflict by the end of the novel, but she has made a real connection with Quentin that is different than the kinds of connections she had in Florida. 

Of course, as with any longer narrative such as a novel, there are more than one conflict, internal as well as external. But, the main conflict that propels most of the narrative is the condition of the relationship between Quentin and Margo.

After being childhood friends, Quentin Jacobsen, the protagonist, loses touch with Margo Spiegelman; however, Margo Spiegelman, re-appears one night at Quentin's house, inducing him to join her on a night of vandalism as acts of revenge. The two teens succeed in their daring mission which includes breaking into Sea World; however, after Quentin returns home and tiptoes to his room, his mind "booming with the things I would say to her at school" the next few days, he discovers that his childhood friend is missing.

Nonetheless, Margo has left some clues behind; so, Quentin elicits the aid of his friends Marcus, "Radar," Lacey, and Ben to help him find Margo. Having found Walt Whitman's volume of poems, Leaves of Grass, Quentin discovers clues to Margo's whereabouts, such as a map with holes that lead him to Algoe, New York. Along the way, there are some serious conflicts among the friends, even ones which could possibly lead "to the death of everyone," but all these conflicts are resolved when Quentin and his friends arrive and find Margo, who is writing in a black notebook. Surprised that they have traced her, Margo begins to explain. The final paragraph provides the resolution to the novel:

I feel her hands on my back. And it is dark as I kiss her, but I have my eyes open and so does Margo....even now there is an outward sign of the invisible light....our foreheads touch as we stare at each other. Yes I can see her almost perfectly in this cracked darkness.

Both Margo and Quentin have been wounded from their young experience of discovering Robert Joyner, who had killed himself in a park. But, now together "in this cracked darkness" of memory and trauma from their youth, they can heal each other.

The most significant conflict in the novel is the internal that both Quentin and Margo share. When they are both nine years old, they discover the body of a man who had died by his own hand lying in the park they had gone to play in. The rest of the story is about the internal conflict of how and how well they each adjust to this traumatic event.