Paper Towns takes place in and around a fictional subdivision called Jefferson Park, located in suburban Orlando, Florida. The novel focuses on the narrator and protagonist, Quentin "Q" Jacobsen, and his neighbor, Margo Roth Spiegelman. As young children, Quentin and Margo one day discover the corpse of Robert Joyner, a divorced man who has committed suicide, in the park. Following this incident, the novel flashes forward to present-day Quentin and Margo, who are now high school students that have grown apart from each other. However, a month before their high school graduation, Margo shows up at Quentin's bedroom window with black face paint and clothes in the middle of the night. She has devised a revenge mission on a group of people who she feels have hurt her over the course of her high school career. The mission has eleven parts to it. Margo needs someone and more importantly, a car, to help her complete the tasks. So, she convinces Quentin to sneak out and help her seek revenge.
To begin their mission, Margo and Quentin head to a local Walmart to purchase a list of items that they will need to complete their plan. After they have purchased all of the necessary materials, Margo and Quentin visit her ex-boyfriend, Jase, and her best friend, Becca, to begin part one of their mission. Jase cheated on Margo with Becca. Thus, to get back at both of them, Margo has Quentin call Becca's parents to inform them that their daughter is currently having sex with Jase in their basement. As a naked Jase attempts to escape the house and wrath of Becca's dad, Quentin takes a picture of him. Margo and Quentin then break into Becca's home, graffiti a blue "M" for Margo on her wall, and leave a dead catfish in her basement to symbolize her betrayal. After the incident with Becca and Jase, they visit Karin, a minor character in the novel, and leave her a bouquet of flowers. Karin is the character who informed Margo that Jase was cheating on her. Upon the revelation of this news, Margo cursed her out in disbelief.
Following the completion of the second part of their mission, Quentin and Margo go to Jase's house, break in, graffiti a turquoise "M", and leave him a fish. They then visit Lacey, one of Margo's best friends and a major character towards the latter half of the text. Margo has always felt that Lacey had never been a good friend to her because she had often ridiculed her and made backhand comments about her physical appearance. Margo and Quentin break into Lacey's parked car. They purposely leave the fish under her car seat and graffiti a blue "M" on the roof of her car.
At 3:15 AM, they sneak into the SunTrust bank building and enter a conference room on one of the higher floors to see a panorama of Orlando. Here, Margo, for the first time, refers to Orlando and their subdivision as a "paper town". She describes it as "fake" and "not even hard enough to be made of plastic." Once they leave the SunTrust building, Margo gives Quentin the option to choose any person that has bothered him over the years to get revenge on. He chooses the school bully, Chuck Parson, who has taunted Quentin since middle school. For the last three years of high school, he stopped bullying Quentin at the request of Margo. Nevertheless, Margo and Quentin proceed to get revenge on Chuck. They sneak into his house, remove one of his eyebrows with hair removal cream, and slather Vaseline on all of the door handles in his home. After getting revenge on Chuck, they break into SeaWorld, where they are caught by a security guard for trespassing. However, Margo uses her persuasive abilities to get Quentin and herself out of any serious trouble.
Following their trip to SeaWorld, Margo and Quentin return to their homes around dawn. After their excursion, Quentin, who barely makes it to school on time, spends the entire day thinking about how things have changed. He wonders if Margo will start hanging out with him and his friends, Ben and Radar. However, Margo does not show up to school that day or the following. After she has been missing for three days, her parents file a police report. Margo has run away four times before in the past, so her parents are more frustrated than worried about her. Her mother even reveals that she plans on changing the locks, so that regardless if Margo decides to come back, she will be unable to. Due to the fact that Quentin was the last person to see Margo, he is questioned by a private investigator. He does not reveal much. However, soon after his conversation with the private investigator, Quentin notices a poster of Woody Guthrie taped to the back of Margo's bedroom shades. As soon as her parents leave her house, Quentin, Ben, and Radar bribe her little sister, Ruthie, to let them in, so that they can search through her room. They soon discover that the poster leads them to a song called Walt Whitman's Niece. This then leads them to Walt Whitman's poem "Song of Myself", which is a part of his poetry collection Leaves of Grass. In her room, Margo provides a copy of the poem with highlighted sections. Quentin believes that Margo has left the highlighted sections as clues for him to find her. Thus, Quentin spends countless days and nights reading and re-reading the poem to search for clues of her whereabouts. After taking advice from Ben, Quentin, one day, decides to unhinge his door. In the poem, Margo highlights a line where Whitman discusses this. He soon finds a small piece of paper that has the address, "8328 bartlesville Avenue", located in his door. Hoping it will lead them to where Margo is, Quentin and his friends decide to skip school the following day to visit the address on the piece of paper. At this location, they find an old abandoned mini-mall in Christmas, Florida that contains evidence of her recent presence and a morbid message spray painted on the walls. Quentin struggles to analyze the message. On one hand, he believes that it confirms her suicide. While, on the other, he believes that it validates his hypothesis that Margo was entirely too fed up with her "fake" life.
Eventually, the clues lead Quentin to believe that Margo may be possibly hiding out or buried in one of the many abandoned subdivision projects or "pseudovisions" around Orlando. Consequently, he drives to all of the pseudovisions where he feels that she may be hiding, but has no luck locating her. On the day of his graduation, while getting ready, Quentin makes a connection with a map that he found in the abandoned strip mall to the one that he made in an attempt to locate her. He matches up the holes from the tacks in the mini-mall to his map. This leads him to discover that Margo has been hiding in a fictional town in New York called Agloe, which was created as a copyright trap by mapmakers, near the existing town of Roscoe, New York. As a result, Quentin, Radar, Ben, and Lacey all opt to skip graduation, in order to drive to New York to search for her. The group is put under a time constraint, as Quentin discovers in the Omnictionary page of Agloe that Margo plans to leave the location on May 29 at noon. Thus, they must make the drive to Roscoe, New York in under twenty-four hours.
Once they reach Agloe, they discover that Margo is living in an old, dilapidated barn. Margo is shocked to see them, which angers the group. They expected for her to be grateful of their presence. However, she reacts to their arrival as an unexpected disturbance and begins to scold them accordingly. Margo had not left any of the clues that they used to find her intentionally. She claims that she did not want to be found. Angry at her lack of gratitude, Radar, Ben, and Lacey leave the barn and spend the night at a motel. Gradually, Quentin realizes that the image he had of her was as fake as the one that she had been emitting to everyone else. As a result, he becomes furious at her for wasting his time. His anger forces Margo to argue that Quentin saved her for egotistical reasons. He wanted to be the hero who saved the troubled girl. Ultimately, Quentin accepts that it was unfair for him to expect that Margo would live up to the perfect image he built of her. After their deep conversation, Margo decides to go to New York City. They briefly kiss. Quentin wants to stay with her, but understands that his responsibilities and the nature of his life at home restrict him from doing so. In the last few lines of the novel, Margo and Quentin vow to keep in contact.