Likely ending scenarios include:
The Old Empire is reestablished by any means necessary. Life returns to how it was, mostly. This basically occurs when there are no factions left that are not
allied at the highest level with the Remnant. I don't see many people going that far with them though.
The major powers form a government of sorts of their own, that is probably more like a Federation; how the factions choose to run their own affairs is largely up to them, but they all meet and talk on important matters of security.
One faction or group of factions becomes so powerful that their conquest of the galaxy becomes an inevitability or an unstoppable occurance, rather than something that could happen, but could be stopped.
Individual win/lose scenarios:
The primary "lose" scenario for an individual faction as I see it is basically losing all of their military vessels and their headquarters to enemy assault. In fact, not even the entire destruction of their fleet is required; simply destroying their headquarters may be enough to force them into negotiations.
If a faction surrenders to you, you will gradually recieve control of all of it's ships and planets. Be warned that ships may opt to join other factions rather than willingly work for their enemy. A faction may also be able to evacuate it's leader to a friendly faction to evade defeat, but maintaining their fleet will be hard.
Alternately you can spare them, or possibly negotiate for them to become your vassal, which means you get a cut of their income, their unique technologies (if any), and constant, up to date information on their faction and it's holdings. You see everything they see, essentially.
Or you can just wipe them out entirely, if you're feeling arbitrary.
(or a deus ex machina)
Whilst I'd like to say it's possible that there might be alien invasions in case you all get too complacent and laid-back, I can't see it happening without some uninvolved designers to ensure that nobody knows what they're up against 'til it hits them.