Paper Towns starts with nine-year-olds Quentin “Q” Jacobsen and Margo Roth Spiegelman discover the corpse of Robert Joyner, a soon to be divorced man who committed suicide in the Jefferson Park.
Nine years later, Quentin and Margo grew apart from each other considering that they are neighbors. One night, Margo shows up in Quentin’s window with black paint on her face. She asks Quentin to help her that night with eleven missions to get revenge on the people that have hurt her throughout her high school years. She especially needs Quentin's car and assistance driving. Margo convinces Quentin to take his mother’s minivan, sneak out of his home on a school night, and help her seek revenge.
Margo takes Quentin to an adventure filled with fish, vandalizing, spray-paint, breaking into SeaWorld, and waxing a bully’s eyebrow while sleeping. After her eleven things are completed, Quentin is glad that he is back to being friends with Margo. The next day, Margo never shows up to school or the next three days. Because Margo had already run away from home, her parents are worry-free since they expect her to come back. Quentin was the last person her parents saw her with when her father found her in Quentin house at night. A private investigator asks some question about where Margo could have run away. He notices a poster of Woody Guthrie taped to her bedroom shades. When her parents left home, Quentin bribes Margo’s sister, so they can investigate her room. The poster leads them to a song called “Walt Whitman’s Niece." The song leads them to a poem called “Song of Myself,” by Walt Whitman. In Margo’s room, there is a copy of the poem with highlighted text. One day, Quentin unhinges his door and finds another clue: an address. The next day, Quentin and his friends skip school and drive to the address left by Margo. When they arrive, they find an abandoned mall. Inside Margo left a message painted in the walls that says, “You will go to the paper towns and you will never come back.” Quentin believes that this is Margo’s way of confirming her suicide while his friends believe it means she was tired of her fake life.
Quentin spends a stretch of time looking for more clues with no success. On the day of his graduation, he looks at the map of New York he found in the abandoned mall. The map has pinholes - one of them in a place called Agloe, New York. He looks up Agloe on the Internet and finds that Agloe is a copyright trap, and that its population rose up from zero to one - until of May twenty-ninth. Quentin, Ben, Lacey, and Radar skip their graduation to drive to New York to find Margo. Since he knows Margo changed the population on the site, they have to arrive at Agloe in less than one day.
When the gang arrives in Agloe, New York, they find Margo living in a barn. Margo is shocked to see them since the clues she left weren’t intended to find her. Angry at her reaction, Radar, Lacey, and Ben leave the barn and check into a motel. Quentin learns that his vision of Margo was fake - similar to the one she had been projecting to everyone else she met. Later, Quentin tells Margo that he was mad because she made him waste his time. Margo tells him that he really saved her because he wanted to feel like the superhero saving the girl. He later accepts that it was obvious that he didn’t expect Margo to live the image he had of her. They both say that they love each other and they kiss. Later, Margo tells him to come with her to New York but Quentin tells her that he has a life back in Orlando. Margo and Quentin say their last goodbyes and promise each other to keep in contact.