In The Chrysalids we see that some kind of tragedy has happened, and that the remaining people live under the strict commandments of the Old Testament. They are led by Joseph Strorm, a fanatical patriarch, whose son is David. The remaining people believe that all people must be the "norm" and anyone that is different should be done away with. Joseph has killed people he considered not normal. David has a secret ability that no one knows about; he is telepathic, and if his father and the others found out, he could be killed. David meets Sophie, a girl with her own secret. She has six toes, and her family is petrified that David's father will find out.

In chapter 5, David and Sophie are down by the lake when another boy comes along. While they are talking, the other boy sees the wet footprint that Sophie just made. David realizes that the boy has seen that Sophie has six toes, and knowing that the boy will tell, David hurries Sophie home. In the night, Sophie and her family escape, but David is left to face his father. He tries his best to keep the secret, but when he is whipped, he finally admits where Sophie has gone. David is upset with himself for not being able to protect Sophie.

I don't know where my mother was, perhaps she was afraid of my father. It was Mary who came, and made little comforting noises as she dressed my back. She wept a little as she helped me into bed, and then fed me some broth with a spoon. I did my best to put up a brave show in front of her, but when she had gone my tears soaked into my pillow. By now it was not so much the bodily hurts that brought them: it was the bitterness, self-contempt, and abasement. In wretchedness and misery I clutched the yellow ribbon and the brown curl tight in my hand. "I couldn't help it, Sophie," I sobbed, "I couldn't help it." 

David has tried so hard to protect Sophie, but his father is ruthless and cruel and has the answer beaten out of him. David doesn't realize that the toughest part is yet to come.