After English supply ships failed to reach Roanoke Island. The colonists returned to Croatoan. And were never seen again.
John white stayed with the colonist's as they were slowly losing supplies. So John white leaves the colonist's alone to get supplies. He doesn't come back in time so all the colonist's leave to go back to Croatoan.
The colonist's left after John White leaves because John didn't come back in time with the supplies. So they left to go find supplies themselves. They never saw John White again.