In the first episode, Gates begins to piece together the family histories of four of the participants. The episode explores the post-World War I "Great Migration" of African-American families from the South to northern cities like Detroit and Chicago, as well as the experiences of those who stayed in the South during the period of Jim Crow segregation. Gates also begins to examine his own familyÕs past, recounting the discovery of a box of photographs and heirlooms that sparked an obsession with his ancestry.
Episode two travels back to the end of the Civil War to look at how African Americans defined their freedom after slavery. Gates reviews courthouse records of land acquisitions, documents from the Freedmen's Bureau and the 1870 census -- the first in which African Americans were counted as citizens, not property -- to trace his guests' lineages through Reconstruction. Gates' personal story continues as he seeks to confirm a family legend -- that a white slaveholder is one of his 19th-century ancestors.
Professor Gates' research becomes even more difficult as he continues back through the Colonial period of American history. War service records and ways of recording property during slavery's apogee -- such as inventories and sales or gifts of slaves -- help fill in the participants' family trees. In West Virginia, Gates learns from a court transcript about the legal struggle of his ancestor Isaac Clifford, a free man who was kidnapped and accused of being a runaway slave.
When the paper trail runs out, Dr. Gates visits scientists who are using DNA analysis to trace ancestral roots. With DNA results and genealogical research in hand, Gates meets with leading historians of the slave trade, and along the way, he learns more about his own ancestry. Finally, Professor Gates and one guest journey to Africa, where they visit the port from which the participant's patrilineal ancestor was most likely shipped into slavery, and meet local tribal elders, who may be the participant's long-lost cousins.