Chapter 1 begins when the main character, David, is a young boy, narrating in the first person in the past tense. He confides in his older sister, Mary, about a dream he has about a fantastic city he has never seen before. Mary advises David not to tell anyone about the dream. David meets a girl by the name of Sophie while sliding down an embankment. As they play together, Sophie’s foot gets stuck; while assisting getting her foot out, David discovers that Sophie has six toes. Initially he does not think much of this discovery, but later he realizes that her 6-toed feet are against societal norms and would result in severe punishment if discovered by the rest of society. Sophie’s parents make an agreement with David to keep the fact that Sophie is a Deviant from the rest of society (which is also why Mary told David to keep his dreams private: the Waknuk society might deem him a Deviant otherwise). David starts to wonder why society even has such a norm against Deviants in the first place.
Chapter 2 discusses David’s family tree and his grandfather, Elias Strorm, the founder of Waknuk. Elias' son, Joseph, who is David's father, is an important man in their town and is a very religious individual—as is his wife, Emily. The Strorm’s family life is filled with religious practices. The religion is focused on keeping the “pure” form of humans, as defined by their text Nicholson’s Repentances. Anyone who does not conform to the norm is considered Deviant. Most Deviants live in the Fringes, the area outside of Waknuk and the surrounding farming communities. As a farming society, Waknuk is also concerned with destroying any genetically mutated plant or animal, known as Offences. For mutant crops, they are burned. Mutant animals have their throats slit at dawn.
David becomes good friends with Sophie. They discuss the lives of the Old People, with each of them accounting for what their elders have told them. David, at one point, while doing a tedious task, says in the heat of the moment that he could have managed the task better if he'd had another hand. As a result, David is punished by his father and is made to repent and to seek forgiveness for his statement. David has a dream at the end of the chapter in which Sophie is being purified/sacrificed like an “Offence” and that his father slits Sophie’s throat with a knife.
Chapter 4 begins by introducing Uncle Axel into the novel. He is portrayed as an individual who cares about David’s well-being, and David confides in him about his telepathic abilities to communicate with other nearby people, including David’s cousin Rosalind, via “thought shapes." Uncle Axel tells David sternly not to let anyone else know about his telepathic abilities. An invasion from the Fringes occurs in Waknuk. Gordon Strorm (or the "Spider-man"), who is Joseph’s brother and who was banished into the Fringes, meets David briefly. After the Fringes incident passes, the Inspector and Joseph disagree over the deviance of Angus Morton’s great-horses, which are larger than normal horses, but government-approved. The chapter ends by telling the readers more about the status of Waknuk as a society, and David shares that he passes his knowledge from his schooling onto Sophie.
David and Sophie are fishing together in the river when an older child, Alan, sees them. Alan sees Sophie’s footprint and becomes suspicious of Sophie and starts to chase her. David starts a fight with Alan to distract him. Just as Alan gets the upper hand, Sophie hits him with a stone and knocks him out. Sophie’s father, upon hearing of the incident, prepares his family to flee the community. David spends the night in Sophie’s empty home to delay the search for the family. When David returns home, he is questioned by the inspector and his father. Under the punishment and pain inflicted on him by Joseph, David reveals that Sophie is a Deviant.
David tells his telepathic community of friends, via thoughts, about the incident with Sophie. In a conversation with the Inspector, David finds out Sophie and her parents were caught. Later, David confides in Uncle Axel and tells him that he wants to run away because he feels scared about his own deviance from the norm. Uncle Axel convinces David not to run away until he is older, and reasons that no one really knows what the real norm of humanity is. Axel bases this knowledge on his experience as a sailor, where he heard about numerous other societies with mutations that they thought were the norm. Uncle Axel also talks of the geographical aspects of Waknuk and the surrounding badlands.
Emily (David’s mother) gives birth to a baby, who is named Petra. The narration foreshadows that she may have some form of deviance. Petra, nonetheless, is still certified normal by the Inspector since she has no deviating body parts physically. Aunt Harriet, who is Emily’s sister, has also given birth recently, but to a Deviant child. In a desperate bid to get her child certified as normal as well, she goes to Emily and hopes that Emily will swap babies with Harriet to get Harriet's certified as normal. However, Emily rejects her proposal, and brings in her husband Joseph who then accuses Aunt Harriet of concealment and attempt to commit a crime. David eavesdrops on this conversation from the next room. Aunt Harriet is later found dead in a river.
David is upset by what happened to Aunt Harriet. He eventually confides in Uncle Axel. Uncle Axel shares some of his philosophy about how the true image of man is unknown: he points out that the Old People caused the Tribulation; thus, they were not perfect either. At the end of the chapter, the telepathic group, which includes a few other characters apart from David and Rosalind, share their names and locations with each other so that they can be more aware of each other in case of any emergencies.
David discovers that Petra can communicate telepathically when Petra falls in the river and sends out a panicky, thought-blocking signal to all the telepaths. David comes to her rescue, and finds that Rosalind also was drawn toward Petra’s signal, thus endangering them, as people could wonder how they both knew of the danger when no one else heard anything. David dreams again of his father sacrificing an offense, but this time, the sacrifice is Petra. The next day when the telepaths each try to communicate with Petra to educate and warn her about societal norms, she is not able to receive their communications. They decide that she is too young to understand. David talks to Old Jacob about the many impurities in the crops and stock this season, and finds out that Old Jacob thinks all impurities, including humans, should be killed, instead of sterilized and sent to the Fringes.
David and Rosalind are in love, but the parents of both Rosalind and David are separately arranging match-making sessions. One of the telepaths, Anne, announces her plans to marry to Alan. The telepathic group tries to talk Anne out of getting married to a normal person because it puts them all in danger. Anne decides to cut off contact with the group and discontinues communicating with them. David, feeling helpless, confides in Uncle Axel for advice in this situation. Less than a year after Anne marries Alan, Alan is murdered. Subsequently, Anne hangs herself, and leaves a letter to the inspector condemning all of the telepathic group. However, Rachel, Anne’s sister, finds the letter and destroys it before anyone sees it. Michael, who acts as as a leader of the telepathic group, feels Anne’s death was for the best.
Chapter 11 begins with a scene where almost everything is normal in Waknuk. Petra rides her pony into the woods and meets a scary creature. She lets out a loud telepathic cry for help, which attracts the entire telepathic group, and also is so strong that it blocks them from communicating with each other. Thus they are all drawn towards Petra, resulting in their first meeting together physically. Their unintentional meeting catches the attention of another man who is suspicious of why all of them would have come to Petra’s rescue (since he could not hear the telepathic screams that Petra gave off). The telepathic group agrees to take more precautions, and to get ready to flee. David begins to teach Petra how to use her power. Uncle Axel confirms David’s fears that there are people who are suspicious of the telepaths. Also, Uncle Axel also reveals that he is the one who killed Alan, because he suspected Alan knew about the telepathic group.
Sally and Katherine, both of the telepathic group, have been taken into custody by the authorities. David, Petra, and Rosalind escape into the Fringes with Rosalind’s father’s great-horses, along with weapons and food. While they flee, they continue communicating with the telepaths still in Waknuk, namely Michael, who has not been suspected as deviant and who is helping to throw the town search party off David’s group’s trail. Katherine is tortured, and both Katherine and Sally are forced to confess that David, Petra, and Rosalind are telepaths. Petra makes contact with a fa- away woman from a place called either “Zealand” or “Sealand” that only she can speak with due to the distance.
David, Petra, and Rosalind continue on their escape. They now believe Sally and Katherine may be already dead. Michael, still in Waknuk, warns David, Rosalind, and Petra that there is a search party following their trail. Petra continues to communicate with the Sealand woman and finds out that everyone in Sealand can communicate telepathically. As they continue to get farther from Waknuk the land around becomes more wild, and David reckons that they have made it to the Fringes. At the end of the chapter, something falls out of the trees and hits David.
David, Rosalind, and Petra have been kidnapped by the Fringes people and are being taken to meet the Fringes leaders. The Fringe people are not all as strange-looking as David expected: they mostly just look dirty. Michael is with the army of people from Waknuk and is updating David on the army’s whereabouts. According to Petra, the Sealand people are going to rescue them, but Michael is skeptical. David meets Gordon Strorm/the spider-man again, who is the leader of the Fringes group. David fights Gordon because Gordon wants to take Rosalind to bear his children. David is thrown out of the Fringes encampment; Rosalind and Petra are kept there as prisoners.
Chapter 15 begins by David waking up to see Sophie, who saved him and now brings him to her cave/home. Sophie is Gordon Strorm’s romantic partner, and she is jealous that Gordon wants Rosalind over her, because Sophie was sterilized and cannot have children. Sophie rescues Rosalind and Petra from Gordon’s tent by killing the guard watching them.
Chapter 16 begins by illustrating the jealousy and tension between Rosalind and Sophie over David; Rosalind is suspicious about Sophie’s intentions of helping them. Rosalind, Petra, and David continue discussing about their plan of escape and are glad to know that the Sealand people are still on their way. The Sealand woman can finally communicate directly with David, Rosalind, and Michael now that she is getting closer. She explains her people’s view that they are the New People because of their telepathic abilities. There is an invasion carried out by the people of Waknuk against the Fringes, with Joseph Strorm being part of the Waknuk army. Gordon shoots Joseph with an arrow and kills him. Later both Gordon and Sophie are also shot down and killed with arrows. As the Fringes people and the people of Waknuk continue to fight, the Sealand woman arrives in a flying machine. The machine discharges a strange web-like substance over the all the individuals involved in the battle, including David, Petra, and Rosalind, causing them to become stuck in a still position.
The Sealand woman finds Michael, David, Petra, and Rosalind, and frees them from the web-like substance. The web-like substance are threads that contract as they dry up, and have killed everything they touched. The Sealand woman justifies the deaths of all the people around them because they (both Waknuk and the Fringes) are of an inferior species, which she claims are dying out anyway. David and the others are shocked but accept the explanation. There is not enough fuel on the Sealand woman’s machine to go to Waknuk to pick up the only remaining telepath there, Rachel, so Michael decides to stay and go back to get Rachel; they will try to make their way to Sealand together separately. David, Petra, and Rosalind leave in the flying machine with the Sealand woman, and they go to the island of Sealand. The book ends as they approach a city that looks exactly like the one from David’s dream at the beginning of the book.