Luke Garner is an illegal child in his family because he was the third child born. For most of his life, he'd been safe, hiding within the confines of his family's farm. But now, because of his association with a rebel third — short for third child — named Jen, Luke has had to take on a new identity. He is now Lee Grant, a new student to the Hendricks School for Boys. Jen's father, Mr. Talbot, obtained the new identity card for Luke. Mr. Talbot drops him off at the school and advises him to blend in. This is close to impossible since Luke has had no contact with anyone but his family and Jen for his entire life.
Most of the other boys at the school have autism or phobias that keep them from interacting with each other, but some are different. One student, whom Luke refers to as "jackal boy," torments him daily before bed. He forces Luke to do a variety of push-ups, sit-ups and other exercises each night. He also makes Luke call himself names. Luke wants nothing more than to escape from his tormentor and from the classes he doesn't understand.
One day, Luke comes across a door that has been left open. When no one else is looking, he ducks out and runs to the nearby woods. He is ecstatic to be away from the school for even a little while, but knows he can't survive on his own yet. He returns to the school but visits the forest whenever he can and eventually hides spuds and bean sprouts in his uniform so he can plant a garden.
On one excursion to check on his plants, Luke discovers that his garden has been trampled. At first angry that his work has been ruined, he realizes it means that others from the school use the unlocked door for escape as well. Luke hides in the hallway one night and follows a group of boys to the woods. As he eavesdrops on their conversation, he realizes they are meeting with students from the nearby girls' school. It also becomes clear that they are also thirds. Luke comes out of hiding and confronts them about ruining his garden. The others have no clue what he's talking about as none of them have ever seen a garden. They didn't realize what they were stepping on as they snuck back to the school at night. Luke is embarrassed and tries to return to the school, but jackal boy stops him. He tells Luke that the reason he picked on him was to make him tougher. There are a lot of thirds at Hendricks, but they're not used to being in public. Many give themselves away by standing up in class and shouting their real names. The hazing, which includes making the new student shout that he's an exnay, a lecker or a fonrol (all derogatory names for thirds or country people) allows the newcomer to admit who he is out loud, without being revealed as a third. Luke becomes a kind of hero to the others when they learn he knew Jen Talbot. She is legendary to those in hiding because she organized a rally in front of the president's house to change the population laws. She was killed, along with the others at the rally.
Luke is accepted by the group and joins in the nightly meetings. Although happy to have made some friends, Luke is wary of being too trusting. As a result, he doesn't tell the others his real name, insisting they call him by his new name, Lee. Luke learns that jackal boy, or Jason, arrived at Hendricks shortly before he did. The others didn't start meeting until Jason arrived, which was just after the rally in which Jen was killed. Luke is excited when the others start making plans for another rally, but soon becomes frustrated. All his new friends do is talk; they don't focus on what needs to be done.
Luke starts to worry about upcoming finals because he's never figured out what classes he should be taking. Instead he sits in on different ones every day. Jason gets him a copy of his schedule but assures him not to worry about the tests as Jason can hack into the school computer to change Luke's grades. Luke, however, is determined to try and learn something from his teachers. He attends all his classes and begins reading his textbooks. On the night before his first exam, he is too nervous to sleep. When he hears someone get out of bed, he waits a moment before following the person. He brings a textbook with him so he can claim he's trying to find a place where he can study quietly.
Luke discovers Jason talking on a cell phone in the hallway. At first he thinks the boy is talking to others in the subversive movement. Luke approaches Jason to let him know he wants in on any plans, but at that moment he hears Jason admit to being one of the Population Police, authorities who hunt down illegal thirds. When Jason spots him, Luke defends himself with his textbook, hitting Jason on the head and knocking him out. Luke takes Jason to the school nurse, telling her that he fell out of bed and had some kind of fit. He warns the nurse that should Jason become conscious, he may say some strange things.
Luke returns to the hallway where he'd encountered Jason, so he can retrieve his history book and Jason's phone. Unfortunately, someone has stolen it. Luke breaks into the school's office so he can find Mr. Talbot's number. He finds his school records and discovers that not only has his past been doctored to make him Lee Grant, but his time at Hendricks has been falsified as well. He appears to have the same behavioral problems as the other boys. Luke calls Mr. Talbot to ask for help, but because the Population Police may have bugged his phone, he can't be specific about what he needs. He tells Mr. Talbot he has to leave the school because of a problem like he had before. He also says that he has four more problems, hoping Jen's father will understand that there are other thirds that need to escape. Mr. Talbot acts as if he only wants to go back to bed because it's 3 o'clock a.m. Luke thinks he has no hope. He explores the rest of the school, looking for a way out, but all the doors to the outside have been locked, and there are no windows. He and the others are trapped until the Population Police come to arrest them.
In the cafeteria at breakfast, the Population Police arrive. Luke is paralyzed with fear, not even able to open his mouth to call a warning to the others. The police warn the students that punishment for violating the Population Law is death. The punishment for having false papers is death by torture. Mr. Talbot enters with Jason in chains claiming that he is the criminal for whom they've been looking. Jason cries out that he's not a third, but he can name others. He betrays five other boys, including Luke. Mr. Talbot laughs at the accusation, claiming that he's known Luke Grant since he was a boy. He even has a picture in his wallet of Luke and Mr. Talbot's family at Christmas. Files are pulled from the office, which prove the other boys aren't who Jason claimed they were, either.
Later that day, Luke's history teacher escorts Luke to a castle on the school grounds. There he meets Mr. Josiah Hendricks, the wealthy man who began the school. Mr. Talbot is also present. Mr. Hendricks explains that when he was younger he spent much of his wealth on foolish living that cost him both of his legs. When the great famines occurred, the government wanted to restrict food to only the healthy people, but Mr. Hendricks used his money to bribe officials so they came up with the two-child rule instead. Feeling guilty that he had saved himself and his family from death while condemning others, Mr. Hendricks started a school for troubled boys so he could eventually bring thirds out of hiding. They could blend in because the other students would also have social difficulties. Once the thirds made the transition to the outside world, they would move out of the school and start real lives in society. Mr. Hendricks and Mr. Talbot agree that Luke is ready to move on. Luke, however, doesn't agree. He wants to stay at Hendricks and help other thirds make an easier transition to the outside world. They agree, and Luke introduces a few to the pleasures of gardening. Since the Population Laws began because of a shortage of food, Luke figures it will be good for them to learn how to grow food. By the end of the book, he asks the other boys to call him "L." It is a combination of Luke and Lee, which is how he is beginning to think of himself.