You completely skipped over Darth Ruin and his Empire,which comes before the Brotherhood of Darkness and then Bane and is thought to be built from pockets of Sith that survived from this era along with his Fallen Jedi.
All we know from the lore is that this version of the Sith Empire ceased to be,they could have destroyed themselves, they could have been beaten by the Republic, they could tire of war and joined the Republic,hell they could have won the war at some great cost(like a majority of the Purebloods) and put on the face of the Republic. The point is we don't know and it allows for freedom in the lore for the writers.
The Dread Masters are one of many major threats and it's pretty tough to point to them as the begining of the end. The Hutt Cartel is beginning to make a power play, the Star Cabal is still around, Malgus's apprentice is running around probably a bit peeved and we still have the Emperor drama.
You could see it as an expansion for the game 'The Return of the Emporer' or somewhere along those lines