An Early American habitation site is discovered in the foothills southwest of Denver. Excavation at the cavern is supervised by Lisa Trayer, an archaeologist with the Colorado Museum of Natural History. In an effort to secure funding for the project, Lisa agrees to a partnership with the Chapleton Institute, a religious fundamentalist organization that seeks to merge science and religion. ANCESTORS OF GODS describes the science-religion conflict that builds between Lisa and Fred Walcott, the representative of the Chapleton Institute, as work on the archaeological site proceeds.