My theory on what may happen in B5-VS6 is that the Swarm will make a re-appearence in the later episodes and that they will become effectively a third force in the B5 universe and they will not come alone.
The Shadows created weapons that they probably have forgotten about. The Swarm was one, maybe they are aware of others and will align with them. They will want revenge against the Interstellar Alliance for getting rid of their masters and the Drakh for their deception. Also we dont know what the Vorlons created aside from Lyta and others like her.