Owen Birnbaum has attended Martha Doxie School in New York City for a few weeks now, but his weight and high intelligence have made it difficult to find friends. He is teased almost constantly by other students and even a few teachers.
The worst culprit is Mr. Wooly, the harsh gym teacher. Mr. Wooly introduces a new gymnastics unit to the class. To begin, he instructs students, one at a time, on how to do a proper somersault while the rest of the class watches.
Owen realizes that Mr. Wooly is giving bad instructions to the nonathletic boys on purpose so they fall and the class laughs at them. Meanwhile, he ignores the athletic types and allows them to perform somersaults unaccosted. When Owen’s turn arrives and Mr. Wooly tells him to place his head and his hips at a certain angle, Owen objects, stating that anyone could see how these instructions were wrong.
Mr. Wooly responds by strapping Owen into an athletic harness and pulling him across the mats, forcing him to somersault in front of the class. After Mr. Wooly instructs one of the students to unbuckle him from the harness, Owen bursts into tears and is excused from the rest of class.
Owen arrives at lunch to find the table he and his friend Izzy eat at occupied by Mason Ragg, the terrifying new kid at school with a mean reputation. Worse, the treasured three Oreos have been stolen from Owen’s lunch box, and Mason, sitting beside a stack of three Oreos, appears to be the offender. With rumors of Mason’s past violence floating around the school, Owen is too afraid to confront him.
After school, Owen walks home with his sister, Caitlin, who is a year younger and insists on being called Jeremy. Jeremy has joined a club at school called GWAB, Girls Who Are Boys. It is made up of girls who have adopted boy names, wear boy clothes and demand to be treated like boys. Owen wonders how Jeremy has kept her long red hair, as every other GWAB member wears short hair.
On the way home, Andre, one of the athletic boys in Owen’s gym class, catches up to the siblings. Andre suggests Owen talk to his father, a lawyer, who would help Owen with Mr. Wooly. When Jeremy presses for details, Owen dismisses the situation, not wanting Jeremy to worry. Owen and Jeremy continue walking to a demolition site, where they search the rubble for interesting gadgets and pieces of metal that Owen can use in his inventions.
After tinkering with one of these inventions called Nemesis and having dinner with Mom, Owen visits Nima, who lives in an apartment on a lower floor. Nima, a serene man who works as a food vendor outside the Museum of Natural History, is a Tibetan Buddhist who has a small shrine for the Buddha in his apartment. When Owen tells Nima about Mason Ragg stealing his cookies, Nima suggests that Owen deal mercifully with Mason. If Mason continues to steal from him, Owen could invent something to catch Mason in the act.
The next day the cookies are stolen again, so Owen creates a mechanism that works like an animal trap. It snaps down on the wrist of anyone digging around in his lunch box. In class the next day, Owen watches Mason ask for a hall pass and leave. Eager to check how his machine worked, Owen asks for a hall pass and follows, only to find his trap hadn’t been set up but his cookies are still missing.
Back in class, Owen walks up to Mason and demands that he gives back the cookies. Mason claims ignorance, and then questions Owen’s intelligence. The accusation makes Owen wonder whether he is able to operate Nemesis after all. Owen claims to be sick so that he can go home early and work on Nemesis.
Overwhelmed by self-doubt, Owen eats whatever food he can find in the kitchen, including the Oreos Mom told him not to eat, before tinkering with Nemesis. The first signs of the contraption operate correctly, but Owen realizes he needs another piece for it. He heads out to scavenge parts from another construction site.
As he walks through the city, Owen passes a store on Broadway and 85th Street, which he had not visited in some time. The store had changed since his last visit. Seeing the change upsets him, and being upset gives Owen a gnawing hunger that takes him to Nima’s food cart.
Nima serves him dumplings and sits with Owen on the steps of the Museum of Natural History. Owen explains a little of what Nemisis is, a radio telescope. With the help of the large, satellite-like roof of the building next to their apartment complex, which captures the radio frequencies of television signals, digital security recordings, etc., reflected off a nearby dwarf star, Owen is hoping to capture an image from two years prior. First, he needs an amplifier to help clear the images that Nemesis is receiving.
Back at home, Owen finds Jeremy and her friend Arthur, another member of GWAB, who are upset because their teacher wouldn’t let them take an important test unless they wrote their girl names on them, rather than their chosen boy names. Owen attempts a second, simpler trap to catch Mason — this time, putting facial hair bleach in his soon-to-be-stolen Oreos.
The next day, Mason appears with a teacher’s aide in Owen’s gym class and soon joins the other students. Mr. Wooly has planned an obstacle course for the day’s activity, dividing the class into two competing teams. Mason and Owen are placed on the same team. When their team’s turn is up, Mason insists that Owen go last and he himself will go second to last.
While the rest of the team goes through the obstacle course as fast as possible, Mason moseys through. A fire drill sounds before his turn is up, and Owen is excused from attempting the obstacle course at all. Owen begins to think that Mason isn’t such a bad person, until he discovers that his whole lunch box, not just the cookies, is missing.
Over the weekend, Owen buys an amplifier from a garage sale and hooks it up to Nemesis. It clears up some of the frequencies, but it’s not enough. Owen realizes he needs a way to date exactly how old these signals are. He strikes a deal with Arthur, trading a bag of his old clothes for two weeks with Arthur’s collection of Retro TV Magazine, hoping to cross reference enough old TV episodes he picks up from Nemesis to eventually track down a date.
On Sunday, Mom takes Owen and Jeremy out for a boat ride around Manhattan. Jeremy and Owen recall a previous ride on this boat with their birth parents.
Walking to school the next day, Andre warns Owen that Mr. Wooly is planning something more humiliating for him and Mason to endure at their next class, since he is convinced that Mason and Owen somehow knew about the fire drill. Jeremy suggests that the stolen Oreos aren’t such a big deal and asks why Owen doesn’t try harder to lose weight. Owen wanted to believe that Jeremy didn’t care about his being overweight but sees that it does bother her, which upsets him.
During class, Mason requests a hall pass around the same time as he did before. Owen also requests a hall pass and follows him. Expecting a confrontation over his stolen lunch, Owen instead realizes Mason is afraid and trying to hide from him. Mason hurries into a different room and Owen runs into his friend Izzy. Izzy is tall. She has been hanging posters around the school in preparation for the parent show.
Izzy walks Owen back to class. Before returning, Owen checks on his lunch and finds that his three Oreos have been stolen again. Having just followed Mason in the opposite direction, Owen realizes that Mason could not be the culprit.
That night, Owen tells Nima about how his birth parents, who used to own a deli on Broadway and 85th, were robbed and killed by a customer while Owen and Jeremy were in the basement. The woman he and Jeremy are currently living with is the 911 operator who answered Owen’s call. Because the deli’s security system wasn’t properly recording the event, the murderer was never found.
Owen is convinced that Nemesis will allow him to recapture the old signal from the deli’s surveillance camera and finally see the face of his parents’ murderer. However, he needs a better amplifier in order for it to work. Nima listens, then kneels at his shrine to pray for Owens’ parents, as well as their murderer.
The next day, Nima gifts Owen the amplifier he needs for Nemesis to operate. Knowing Nima does not have much money to spare, Owen is touched. Mom invites Nima to stay for dinner. After Owen tests out Nemesis with the new amplifier, it appears to work as Owen expected. Owen is thrilled and shows Jeremy.
While Jeremy knows Nemesis’ intended purpose, she doesn’t seem as enthused. The next day, Jeremy asks why Owen spends so much time on the machine when he knows it could never bring back their parents. The encounter leaves Owen upset, and he begins to binge eat to stop the gnawing hunger, but then stops himself by focusing on his work with Nemesis.
Eventually, Nemesis picks up the frequencies of an old episode of "The Brady Bunch," and when the show goes to a commercial, Owen is lucky enough to catch a trivia question that eventually leads him to the date of the original broadcast: October 15, 2006. This date is 10 days prior to the murder. Owen is filled with the hope that he might be able to bring his parents’ killer to justice.
Owen suggests that Mason skip class and let Owen take the full force of Mr. Wooly’s wrath. As gym class nears, Owen’s nervousness increases, and he goes to the boys' room, a little queasy. In the bathroom, he finds his stolen lunch box hanging from a wire near the ceiling. Owen concludes that Izzy has been stealing his Oreos. No one else is tall enough to hang his lunch box so high.
Mason arrives at gym class, despite Owen’s warnings. Together they observe the new obstacle course Mr. Wooly has set up. Mason advises Owen on how to get through it with the least embarrassment. Owen is surprised to find that the boy everyone said was so violent and cruel is actually trying to be helpful.
Before class can begin, Arthur and the other members of GWAB interrupt the class, all wearing the gym uniform issued for boys. Jeremy is among them, her long hair shorn. While they give their statement of inclusion, Mason seems distracted. Mr. Wooly initially tries to get the girls to leave, then decides a larger audience won’t deter him from putting Owen and Mason through the course. When he announces it’s time to start, however, Mason runs to the exit.
Owen chases after Mason, demanding to know why Mason even came to class if he was only going to run away. Mason only asks that Owen keep him out of view of Mr. Wooly and the rest of their class (who have followed them) before rushing into the boys’ locker room.
Owen isn’t sure what’s wrong, but he does what Mason asks. When the rest of the class and the GWAB members arrive, Jeremy slips past Owen and into the locker room after Mason. Mr. Wooly tries to follow, but Owen steps in front of him. Although Mr. Wooly demands that Owen step aside with shouts and threats, Owen refuses to let him through the locker room door.
Mr. Wooly sends Andre to bring in the security guard to have Owen forcibly removed, but before the guard can arrive, Jeremy comes back out from the locker room. Jeremy explains that Mason has had a seizure, but the fit has passed and he is OK.
The drama takes up the whole class time, and soon a hall monitor finds Owen and tells him the principal would like a word with him. Owen finds Mason sitting outside Principal DeRosa’s office. Mason explains that he ran away because he realized he was about to have a seizure.
When he hears the sound of a train, it is a warning that usually gives him enough time to leave class to find his teacher’s aide or a safe place before the seizure begins — which is why he kept requesting hall passes during class.
Distracted by the GWAB members’ unexpected arrival, Mason waited longer than he should have to leave. Principal DeRosa calls Owen into her office to give his side of the story. She listens, then scolds him for potentially putting Mason in danger, but no other disciplinary action is taken.
After school, Owen takes the family dog for a walk and considers the Nemesis project. He wonders whether he’s ready to see the face of his parents’ murderer. On the way home, he runs into an angry Arthur, who has taken back the videos she loaned to Jeremy. Among the box of videos are the same old TV episodes that Owen has been picking up through Nemesis.
Owen realizes that Jeremy had tricked him into believing Nemesis was working. When Owen confronts Jeremy, she admits that she did it because she wanted him to believe he was succeeding at something. Enraged, Owen goes to his room and destroys Nemesis.
Jeremy confesses that she had been stealing Owen’s cookies as a way to avoid the GWAB initiation of cutting her hair short. They told her she had to prove her commitment to their cause by stealing her brother’s lunch, but she convinced them to let her only steal the cookies.
She had left the cookies at Owen’s usual table that first day, but Mason sat at that table. One day Izzy caught her in the act, but she made him promise not to tell. Eventually she decided having her hair cut was better than deceiving her brother, so she let the GWAB members cut her hair just before their gym class rebellion. Since Jeremy was the one who ultimately gave the speech and also entered the boys’ locker room, the GWAB members made a motion to make Jeremy their president instead of Arthur. After the way they had treated her, however, Jeremy refused and left the group.
Over the next three months, Owen loses some weight and is no longer bullied at school. Owen and Mason become good friends. Owen repurposes the parts of Nemesis to create a brightly colored ferris wheel for Nima’s food cart. Owen eventually lets go of his obsession with finding his parents’ killer and instead prays that the murderer will be found and brought to justice, or at least that he is unhappy for the rest of his life.