America has been devastated by the Annihilation virus, a disease that eliminated civilization as it killed 95% of humanity. Gregg MacDonald, his wife Christine, and his two daughters, Sarah and Leah, are bare survivors in a post-apocalyptic anarchy. After a narrow escape from death at the hands of marauders, they feel compelled to seek sanctuary with the Chosen, a mysterious religious cult secure within a walled, armed compound. Within the compound's walls, they feel secure for the first time in decades and can live in pre-Annihilation normality. But when they learn the secret mission of the Chosen, they have to decide whether they are more secure within the compound than outside it and whether they can commit themselves to the frightening future the Chosen and their charismatic leader, Prophet John, have chosen to bring about. In making this decision, Christine and Gregg have to assess their own basic values, the relationship between their religion and their faith in science, and the degree to which they are willing to put their daughters at risk. Ultimately, they have to decide whether to leave most of what they love and help the Chosen pursue Prophet John's dangerous dream.