Well I reckon from the fact that the Vasari are running from whatever enemy destroyed their empire, and forced the remainder of their species to up and flee for however many hundreds or thousands of years they have been running for now. I also reckon that war isn't over at all, that we play as the vanguard/main fleet of the Vasari, and the dark fleet that gets mentioned so often, supposedly the remnants of their old war fleet, isn't as scattered as the game makes out. What I like to think is that the dark fleet is their rear guard, and still fighting/delaying their ancient enemy to give the main fleet time to gather supplies before resuming the flight. Anyways, that is more just based on my own thoughts on the back story.
I think that whatever is chasing the Vasari, is the fourth faction of the game (ignoring pirates) and that if/when Sins gets a proper sequel, or maybe even the next expansion pack, from how the start cut scene of Rebellion so directly mentions the impending arrival of their enemy, that this will be the main theme. That the threat has arrived. Why I think it'll be a fourth faction? Just a feeling. And if it is a fourth faction, I think it will be robots. Either that, or some spiritual sort of entity. Lol we have techno aliens, trady humans and magical meta humans, so robots feels like it would fit 
Though all of that is speculation and opinion. I do believe it will be explained in the next game/expansion though, so you'll have a solid answer in a year or two. maybe three. Lol
