Since the sensational 1994 discovery of James Fort, the first permanent English settlement in the New World, excavations have revealed palisade walls and numerous buildings, along with remarkable clues about the Anglo-American culture that started with the landing of colonists on Virginia’s Jamestown Island in 1607.

But because much of the original fort is buried underneath a Confederate earthwork called Fort Pocahontas, these discoveries forced a painful historical and archaeological trade-off. To reveal James Fort, nearly half of Fort Pocahontas has been removed.

In the process, invaluable traces of America’s founding have been discovered right next to remains from the Civil War. “It’s probably the only place you would have a story like that,” says Colin Campbell, president of Colonial Williamsburg, citing the conjunction of two pivotal moments in U.S. history. “I think it’s absolutely fascinating.”...