GLOUCESTER, Va. — A farm field overlooking the York River in Tidewater Virginia is believed to be where Pocahontas interceded with her powerful father Powhatan to rescue English Capt. John Smith from death.

That’s a fanciful footnote for many Virginia Indians, historians and archaeologists, who say the real story is that this land was the center of a complex, sprawling empire ruled by Powhatan long before the first permanent English settlement in American was founded in 1607. It was called Werowocomoco, which roughly translates to a “place of chiefs.”...