The first idea is to have four campaigns with the eight playable factions (in some scenarios you would get NPC allies like the Tholians):
A Federation / Klingon Campaign, where you follow some strange events happening in the Alpha Quadrant.
A Romulan / Ciadan Campaign, where you meet the Romulans and initiate an epic alliance as well as some conflicts that won't be revealed yet.
A Borg / Iconian Campaign, where you first siege the Iconian Home system thousands of years ago and then, far in the future, return with the Iconians...
A Noxter / Dominion Campaign, where you lead the Noxter through the Gamma Quadrant and rebuild the Dominion Order.