Captain Nobody is narrated by Newt Newman, a thoroughly average ten-year-old. The book opens with an ominous prologue in which Newt is falling from somewhere very high. As he falls, he remembers that everything started on the morning of the Big Game.
The narrative flashes back to the last Friday in October. Everyone in Newt’s hometown, Appleton, is excited for the Big Game between the local high school football teams, and no one is more excited than Chris, Newt’s older brother and local football hero. Newt feels inadequate next to his star brother and ignored by his workaholic parents. He is similarly ignored at school, except for his two friends Cecil and JJ. Before class, the three discuss their Halloween costumes, but are disappointed by how boring they are. They decide they must all come up with a costume that matches their “inner other.” Newt struggles all day to come up with a good costume, even as his parents take him to watch Chris in the big game.
Newt accidentally gets locked out of the stadium during the final quarter, but sees his brother score the winning touchdown despite being tackled. But Chris does not get up. At the hospital, the doctors inform Newt’s family that Chris is in a coma. Over the next few days, Newt replays the tackle over and over. On Halloween, Cecil and JJ come over, but Newt admits he still doesn’t have a costume, only his brother’s jersey. Cecil and JJ transform the jersey into a superhero costume and all three go trick-or-treating. After being asked who he is by an adult, Newt takes his brother’s initials, C.N., and declares himself Captain Nobody.
The next day, Newt wears his Captain Nobody costume to school. His classmates mock him and the school administration worries he’s coping poorly after his brother’s accident. That night, Cecil calls for Captain Nobody, asking Newt to help him retrieve a cool, old bass drum from the top of a dumpster. Newt is afraid of heights, but Captain Nobody isn’t. They get the drum and are interrupted by Mr. Clay, an old man with Alzheimer’s who has gotten lost. Captain Nobody escorts Mr. Clay home. Mr. Clay explains to his relieved wife that Captain Nobody rescued him.
Newt and his dad discuss Chris. He isn’t yet well enough to have visitors. Newt’s parents think the Captain Nobody persona is funny and harmless, and his classmates and teachers even get on board. At school, Newt is confronted by Ricky, the cousin of Reggie, the player who tackled Chris. He and Newt argue, but the rest of Newt’s class come to his defense. Captain Nobody has made everyone braver. Later, JJ calls for Captain Nobody, distressed by grammar mistakes on the sign for Sullivan’s Jewelry store. Annoyed, Captain Nobody agrees to talk to the owner. When he enters the store, he realizes he has interrupted an armed robbery, and with the robber distracted, the store owner manages to pull the alarm. The robber flees. Newt and JJ run away before the police arrive. That night, Newt is mentioned on the news, but only as “the little guy” or “midget” not as Captain Nobody. That morning, he hears the robber has been arrested. He also discovers a crumpled medical report in the trash, which tells him Chris may not ever wake up.
The next day after school, while acting as an ambassador for Ferocious the ferret, Chris’ team’s mascot, Newt is set upon by Ricky and his friends. In the chaos, the ferret escapes onto the highway and, as Captain Nobody, Newt halts the oncoming traffic. Just then, a very small plane makes an emergency landing on the highway. Though the local news seems unclear on whether Captain Nobody is a hero or villain, Newt is ready to retire the persona. As he dreams that night, he recalls his brother’s accident, which he saw from a special vantage point. He remembers that it was Darryl, one of Chris’ teammates, who caused the accident.
The next morning, Newt prepares to visit Chris, when the news reports that Reggie is on the local water tower, about to commit suicide over his guilt in causing Chris’ coma. Newt, the only one who knows the truth, puts on his costume. Newt goes to the water tower. CC and JJ help him evade the police and he reaches the top. He learns that Reggie is not there to kill himself, but got stuck trying to graffiti the tower. Captain Nobody helps Reggie get loose, and as they climb down, Newt falls. Thankfully, he lands on a rubber mattress, but then Reggie lands on top of him.
In the hospital with a broken ankle and ribs, he sees the news report on his stunt at the water tower. He tells his parents that Reggie was not responsible for Chris’ coma. While visiting his brother for the first time, Chris finally wakes up. After he and Chris recover, Newt leads the victory parade as Captain Nobody.