I recently slaughters all the Imperials in Fort Greymoor , waited a few days & even continued doing quest & such. But still only Agnis remains no Bandits have taken over the fort. Neither has the Imperials shown back up, Will they not show up again after I killed them all? I ask because I figured they would show up again, just like the Bandits would back when I first played Skyrim on my PS3 back in early 2012. I am currently playing on PC now.

This fort is outside Whiterun right? Past the tower the dragon attacks? Agnis is a DB target I believe which is why she remains. Nazim will have you deal with her later.