Fallout 3 Big town - the people of the town vanished / died?

i completed big trouble in big town, brought the 2 prisoners back, then went off and did something else, I then used big town to "fast travel" to get somewhere else undiscovered, so while at big town thought i would have a look around, but everyone is missing, went in building in case they were hiding, came out and got attacked by super mutants, wheres my little villagers gone? or is it part of the game that they have to die?