Reverend Ballou is telling the Christian Biblical story of Joseph and Mary. In the Christian story, Mary’s baby isn’t Joseph’s—she becomes pregnant without having sex, by a miracle, after agreeing to give birth to God’s son Jesus Christ (who is also, mysteriously, God). The novel ignores the Biblical Joseph’s non-paternity to emphasize that Joseph Brook identifies with the Biblical Joseph as a young, overwhelmed father who wants to provide for his pregnant partner. Joseph Brook’s question to Reverend Ballou, “where the hell were they?”, may refer to his feelings of abandonment during any one of his traumas, e.g. his mother’s death, Madeleine’s death, or his implied sexual assault at Stone Mountain.