Paper Towns follows protagonist Quentin Jacobsen in his coming-of-age and first love. The novel starts with Quentin and neighbor Margo Spiegelman spending time together as young children. They develop a strong friendship and share many childhood secrets and adventures. Now attending the same high school, the two have grown apart but nonetheless maintain a passing acquaintance.
The second part of the novel describes Quentin and Margo reconnecting as close friends. Margo enlists Quentin's help in pulling off a series of pranks against a number of her high school foes. As the two engage in this series of ever-escalating pranks, they re-learn each other's personalities and share a more adult emotional and romantic intimacy. Quentin starts to realize that Margo's personality is unstable and superficial, but nonetheless continues to romantically idealize her.
After the two have taken revenge on each of Margo's enemies, Margo suddenly goes missing. Quentin and his friends determine to find her and begin to search for clues. The group finally locates Margo, who is living alone in seemingly impoverished and dangerous circumstances. However, Margo resents the group's "rescue," claiming she is not in any trouble and doesn't need their help.
Eventually, Quentin becomes thoroughly disenchanted with Margo. The two end on amicable terms, but Quentin will never again experience the romantic hopes and illusions he once had for her. His coming-of-age is marked by romantic disillusionment and the onset of a more mature perceptiveness and realism.