What happens to Mark in The Chrysalids?
Very interesting question. Of course, the text does not contain any answers to this question. All we are told is that Rachel has not heard anything of Mark for some time. I think it is safe to assume that he has not been captured and tortured, because he would have been able to let Rachel know if this were the case. Perhaps we need to look further back in the novel and remember the death of another member of the group - Walter Brent. Remember when David asked his Uncle Axel to find out about the sudden disappearance of one of their group? Uncle Axel comes back and tells David:
"I found out there was a boy killed just about the time you said. Walter Brent his name was, about nine years old. He was fooling around when they were felling timber, and a tree got him, poor lad."
Perhaps, then, this is the key to explaining Mark's disappearance - he may have died in an accident, explaining why Rachel has not heard anything from him.