The Chrysalids begins with a conversation between David and his sister Mary Strorm about David’s dream of a city he has never seen before. Mary warns him not to tell anyone about the dream because in Wanuk, the town where they live, it is best not to stand out. This proves to be good advice when David meets Sophie, who has six toes. According to the Wanukian religion, anyone whose body does not comply with the Definition of Man is a Blasphemy, and must be sterilized and banished from the community. This belief is based on the idea that God makes man in the image of himself, and God does not make mistakes, so anyone who does not look like the Image of God must not be a man, and consequently, must be the work of the devil.
While David has been taught this definition, he has not internalized it, and he sees no problem with the fact that Sophie has six toes. He does his best to protect her, but eventually a boy named Alan sees her six-toed footprint and reports it to the authorities. Sophie and her family are forced to flee, and David learns to take deviations from the norm seriously.
Although David is physically normal, he, too, is a Blasphemy. David, along with a group of eight other people, has the ability to communicate telepathically, or through “thought-pictures.” When David is young, he is not aware of how dangerous this ability could be, but conversations with his Uncle Axel reveal that David would be persecuted for this gift. Uncle Axel is a kind and reasonable man who disagrees with many aspects of the Wanukian religion and supports David, even though it is illegal to do so. David’s father, Joseph, on the other hand, is an orthodox believer and is very willing to persecute anyone, family included, who deviates from the norm.
Years later, David’s mother, Emily, gives birth to a daughter, Petra, who is granted a Certificate of Normalcy. Her sister, Harriet, gives birth around the same time, but her child has a mutation. When Harriet asks Emily if she could switch her child with Petra for a few days in order to obtain a Certificate, Emily and Joseph refuse and throw her out of their home. She commits suicide the next day.
As David and the other telepaths grow older, they learn each others names and develop relationships with another. David and his half-cousin, Rosalind, are involved romantically. Another in their group, Anne, decides that she wants to marry Alan, a non-telepath and the same person who turned Sophie in for her deviation. Much to the protestations of the group, Anne goes through with the marriage. When Uncle Axel realizes that she has told Alan about the ability of everyone in the group, he kills Alan to stop him from telling anyone else. Anne kills herself when she hears the news of her husband’s death.
These two deaths make David nervous about his ability, but he is only forced to take action to protect himself because of his sister, Petra. Petra has extraordinarily powerful telepathic capabilities, but she is too young to be able to control them or even use them consciously. One day, Petra rides her pony into the forest and is attacked by a wild animal. She unknowingly sends incredibly strong distress signals to everyone in the group and forces them to come running to her. The group knows that it is a bad idea to be seen together, but before they can disperse, a man named Jerome Skinner catches David, Rosalind, Katherine, and Sally surrounding Petra. He becomes suspicious about how they all could have known she was hurt.
Soon after, Katherine and Sally are captured by the government, and David, Rosalind, and Petra are forced to flee to the Fringes, the area outside of Wanuk where Blasphemies and Deviations are allowed to live. Michael, Mark, and Rachel, three more telepaths who have not been identified by the government, stay back to pass information on to the fugitives to help them escape. Petra, who has an extraordinary range, makes contact with a woman who is very far away in a land called Zealand (sometimes Sealand). She tells them that she is coming to rescue them, and that Petra must be kept safe at all costs.
As Rosalind, David, and Petra venture deeper into the Fringes, they are captured by a group of men who bring them to their leader, Gordon. Gordon turns out to be Joseph Strorm’s brother and David’s uncle. He is bitter over having been exiled for his overly-long limbs, and wants revenge on Joseph and on Wanuk. Fortunately, Sophie, whom David has not seen in years, is in a relationship with Gordon and helps Rosalind, David, and Petra escape from his camp. Sophie lets the fugitives stay in her cave and hide from the Wanukian forces that are pursuing them.
Eventually, the Wanukians and the Fringe people, led by Gordon, meet in battle. Gordon kills Joseph Strorm. He and Sophie are both then killed in battle. As the battle unfolds, the woman from Zealand arrives in a spaceship that casts thin strands of plastic onto the battlefield below. These strands contract when resisted against, and freeze everyone on the ground in place. The Zealander woman frees Rosalind, David, Petra, and Michael, who has come to help, from the plastic, but allows it to suffocate everyone else on the battlefield. She explains to the group that it is natural for one species to rise up and overpower another, and that she does not feel guilty for killing these people because change is the nature of life. Michael decides to return to Wanuk to find Rachel, and the woman takes Rosalind, David, and Petra back to Zealand, where as it turns out everyone can communicate telepathically.