The book features two different narrators, both named Will Grayson. The odd-numbered chapters are narrated by a Will Grayson who lives in Evanston, at the northern edge of Chicago. The even-numbered chapters are narrated by a Will Grayson who lives in Naperville, a Chicago suburb. Both Will Graysons are high schoolers. 

The Will Grayson in Evanston (“Evanston Will”) has a best friend named Tiny Cooper. Tiny is described as a large and flamboyant gay man. They have been friends for years. While Tiny has had many boyfriends, Will tries to maintain some distance from most of his peers. Will lives by two rules: 1) “don’t care too much” and 2) “shut up.” Will goes to a rock concert with Tiny and meets Jane, one of Tiny’s friends. He likes Jane, and they share common taste in music. 

The Will Grayson in Naperville (“Naperville Will”) has few friends and suffers from depression. Even though he takes prescription medication, he is still very negative and destructive. He has a close friend, Maura, whom he does not treat very well. She expresses interest in dating him, but he is gay and does not want to tell her (or anyone). He has also been in an online relationship with a boy named Isaac, who lives in Ohio. Will shares everything with Isaac, who is supportive and understanding. Maura confronts Will at the drugstore while he is working and asks him if he is gay. He is rude to her, and their friendship suffers further. He and Isaac plan to meet for the first time, in a week.

Tiny tells Evanston Will that he has written a musical called Tiny Dancer (which is about himself). He wants the student council to fund the production at the school. Jane flirts with Will, and he defaults to his usual emotional avoidance. Will, Tiny, Jane, and their friends Gary and Nick, head into the city to see another concert. Will decides that he might have feelings for Jane, and so he emails the band and asks them to dedicate a song to her. Due to a complication with Will’s fake ID, he is unable to get into the show, and his friends go in without him. While waiting for the concert to finish, Will goes across the street to an adult bookstore, hoping that he will have a funny story to tell his friends afterward. 

Evanston Will feels uncomfortable in the adult bookstore. Naperville Will arrives to the same adult bookstore, as it is where Isaac said they should meet. Naperville Will does not know why Isaac would choose the location but wanders in the store looking for Isaac. When he hears Evanston Will’s name read aloud at the cash register, he is surprised, since it is his name, too. Evanston Will leaves and Naperville Will follows him outside. Eventually, Naperville Will receives a call from Maura. She tells him that Isaac does not exist. She created Isaac’s account and has been talking to Will. She says that it is because he would not tell her of his sexuality. Naperville Will has an emotional breakdown. Evanston Will tries to comfort him but finds the situation very awkward. When Tiny calls, Evanston Will tells Tiny that he should come help.

At Millennium Park, Naperville Will and Tiny discuss all of Will’s problems. They kiss and decide to start dating. Meanwhile, Evanston Will spends time with Maura, who tells him that she ran into an ex-boyfriend. She believes that the ex-boyfriend is responsible for the song that the band dedicated to her. Will does not tell her otherwise.

Naperville Will completely ignores Maura. He and Tiny text and instant-message to communicate and become close quickly. Tiny’s musical gets funding from the student council, but Tiny decides to change the title to Hold Me Closer, and to make the production about love, instead of his own life. Evanston Will is disappointed that Tiny did not tell him that Maura was possibly in a relationship. 

Tiny visits Naperville Will’s home and gets along well with Will’s mother. Will is conscious of how wealthy Tiny’s family is and feels ashamed of his own house. They get along well otherwise and kiss. With the musical in full production, Evanston Will cannot find any of his friends in the lunchroom and instead goes to the auditorium with his tray of food. Once there, he hears Tiny instructing Gary, who is playing a character based on Evanston Will, that he needs to be more pathetic and irritating. Will becomes upset and leaves. He expects that Tiny will chase after him to apologize, but he does not.

Jane visits Evanston Will and tells him that she is no longer with her boyfriend. They kiss. Will invites her in for dinner. Tiny visits Naperville Will, and they get into an argument about how privileged Tiny’s life is and how difficult Naperville Will’s life is. Tiny tries to explain to Will that his life is not easy, and no one appreciates everything that he does. Will lets Tiny leave without apologizing, ending their relationship. 

Naperville Will talks to Maura and apologizes for being a bad friend, while not forgiving her. He then contacts Evanston Will to find out how Tiny is doing. They talk about the musical and how Tiny is very stressed out. Naperville Will comes up with a plan and drives to the musical with his friend Gideon. The musical shows scenes from Tiny’s life, and the songs are well received. At the end of the production, while Tiny is alone in the spotlight and the audience is waiting for the curtain call, Naperville Will yells out to Tiny. He tells Tiny that he appreciates him. Other people in the audience also tell Tiny that they appreciate him, including Jane and Evanston Will.