Set in Chicago, Illinois, Ghost Boys begins with the novel’s protagonist, twelve-year-old Jerome Rogers, looking at his own body lying dead in the snow. A ghost now, he watches his distraught mother arrive at the scene as police warn the crowd of angry and upset locals to stay back. Jerome remarks that he's famous now.
The story goes back to the morning of December 8, when Jerome is alive. He walks to middle school with his younger and more popular sister, Kim. Jerome avoids a trio of bullies who harass him daily. Moving ahead in time, Jerome is present at his family's apartment. His grandmother compares his killing to that of Emmett Till in 1955. Till was also a Chicago boy. His father compares Jerome's killing to that of Tamir Rice in 2014 and says that white men have been killing Black people since slavery. That night, Jerome meets the ghost of fourteen-year-old Emmett Till in his parents' kitchen. At Jerome's funeral, Emmett appears and warns Jerome not to go inside the church.
We move back in time to December 8, and Jerome is at school. He meets Carlos, a new student from San Antonio, Texas. Carlos tries to befriend Jerome, who knows that as a new student he will be a prime target for the bullies. At lunch, Jerome rushes Carlos through the cafeteria and shows him how to eat lunch while hiding in a toilet stall, away from bullies. The bullies find the boys, however, and Jerome tries to defend Carlos when the bullies get hold of him. The chaotic scene ends with Carlos pulling out a gun that he somehow got through the school's metal detectors.
The story moves ahead four months to April 18. Jerome's ghost sits in to watch the preliminary trial, where they will determine whether there is enough evidence to charge Officer Moore for killing Jerome. The white cop claims before the judge that he feared for his life and believed Jerome was a large, hulking adult with a real gun. He did not know he was a child. Jerome realizes Sarah, Moore's daughter, can see him and speak with him.
Returning to December 8, Carlos scares off the bullies by waving his gun around. Once the bullies leave, Carlos reveals to Jerome that the gun is just a plastic toy. The boys laugh. Jerome, as a ghost, visits Sarah at home. She talks about how lonely she is. Her father enters the room and Sarah questions him about Jerome being twelve and the same height as her. Her father gets angry and slams the door.
After school on December 8, Carlos insists that Jerome borrow the toy gun so he can play make-believe with it. Jerome is reluctant to borrow the gun, and Kim also tries to talk him out of it. But Carlos is trying to make a kind gesture as a new friend, and Jerome likes the idea of pretending to be in Rogue One. Jerome accepts it.
In Sarah's bedroom, Jerome is frustrated to learn Sarah's father is on paid leave following the shooting. The ghost of Emmett Till arrives and shows Sarah and Jerome that there are thousands of other "ghost boys." Outside Sarah's window, thousands of shadows appear and look into their souls. Alone together, Jerome expresses frustration with being a ghost, unable to move on from witnessing his family's pain. Emmett tells Jerome that it's important that Sarah can see him.
On the evening of December 8, Jerome and Sarah watch the video of Jerome's killing together; it has been released online. They see that neither Moore nor his partner attempted any life-saving measures. They simply stood over Jerome's motionless body as he lay dying. Moving back to earlier that day in the courthouse, the 9-1-1 operator is on the stand. She says that the emergency call about Jerome specified that the gun was probably a toy, but this key piece of information wasn't passed on to the reporting officers. It is the same situation that contributed to Tamir Rice's death.
At Sarah's well-funded school, Sarah asks the librarian about Emmett Till, whose death spurred the civil rights movement. After thinking about whether it is appropriate, the librarian shows Sarah photos of Till in his open casket, which his mother insisted on so the world could see how viciously he was tortured and lynched. Meanwhile, Carlos has been walking Kim home after school, and Grandma has been walking her to school. Jerome can see that something is bothering Carlos, though he hides it with a smile.
On the second day of the preliminary hearing, the courtroom reacts in chaos when the prosecutor asks why Moore shot Jerome in the back—evidence that Jerome was running away and not posing a threat to the police. Moore repeats that he took the shot because he feared for his life. After a recess, the judge announces that, as regrettable as Jerome's death is, the police have a difficult and complicated job. She says that it is the court's opinion that there isn't enough evidence against Moore to warrant a trial for excessive force, manslaughter, or murder.
In May, Emmett tells Jerome the story of his killing. Looking into Emmett's eyes, Jerome sees the story like a film. In the summer of 1955, Emmett leaves Chicago to stay with his cousins in Mississippi. His cousins warn him about how he needs to act deferentially around white people in the racially segregated town. Emmett insists he talks to white people all the time in Illinois. Emmett confidently goes into a shop and buys a piece of chewing gum from a white woman; he smiles and thanks her on his way out. The woman is so offended that she alerts her husband and his accomplices, who abduct Emmett from his cousins' home at midnight. They beat him, shoot him in the back, and then tie his body to a wheel using barbed wire before pushing the wheel into the river. At the end of his story, Emmett says that everyone needs to have their story heard and felt.
In the last chapters of the novel, Carlos finally tells Grandma that he was the one who gave Jerome the toy gun. Grandma forgives him and embraces him, saying she shouldn't have let him go play that day, because she knew he was up to something naughty. Jerome visits Sarah, who has disposed of her childish pink toys and bedding and now spends all day on her computer. She shows Jerome that she has made a website that collects information on Black boys like Jerome and Emmett who have been wrongly killed because of racial prejudice. Jerome implores her to talk to her dad again, who she holds responsible for unjustly killing Jerome. She goes down to speak with him, asking if he'll help her with her website project. He agrees to help.
On November 1, Carlos's family has a picnic with Jerome's family on Jerome's grave. They eat food and decorate Jerome's tombstone, celebrating the dead in the Mexican Day of the Dead tradition. The cemetery fills with other ghost boys. Jerome's narration returns to the day he was killed. He details how he was playing in an abandoned lot, pretending to be in a first-person shooter video game, when a car came speeding toward him. He turned to run and was immediately shot down, the bullet wounds like two sticks of fire in his back. In the last chapter, Jerome asks the living who have heard his tale to "bear witness" and make the world a better place.
