I'm starting up a series that runs episodes between the factions. Problem is I can't have the 2 factions NPCs shooting at each other. In what is supposed to be a joint operation of sorts. Is there anyway we can get a way to change the enemies from friend to foe or vice versa?
Not really, however you can take a friendly NPC and change the "costume" so that he looks like a foe.
For example I'm working on a KDF mission where you have to cooperate with Starfleet officers to escape a klingon noble who's completely off his rocker. I made the friendly Feds by dressing orions & klingons as Starfleet officers and the bad klingons by dressing Fed NPC groups as klingons.