Strife with the Native Americans
For hundreds of years, historians believed that Native Americans massacred the colonists. And they had good reason to buy that theory, because a chief claimed credit for the bloodshed. In 1609, John Smith, of Jamestown colony and Pocahontas fame, reported to the English that Powhatan (aka Pocahontas' dad) had confided in him that he'd ordered the execution. Add in the Howe affair, plus some early antagonism on the English's part, and you have a convincing case that the Native Americans slaughtered the residents of Roanoke.
The only problem? Historians have turned against this story in recent years, favoring a theory of assimilation instead. Many now maintain that the colonists lived among local tribes after their governor, John White, left on supply run to England. (He took three years to return.) But they still could've met a bloody end that way. The late Irish historian David Beers Quinn suggested that the colonists packed up and joined with the Chesapeake tribe, only to be murdered later by its rivals, who were -- you guessed it -- the Powhatans. AHS might incorporate murderous Native American warriors either way.