Cool idea Jerod. The Parasitic Invaders from conspiracy were referred to as "Bluegills", which I always thought funny as it is neither a gill nor blue. I guess that sounds better than coral nipple, which is actually what they looked like from the outside. I don't know how widespread the use of that particular name was, but I'll use it here.
Actually, I recall all of the Federation Civil War threads and find this to be the most plausible cause. Rermember that the Bluegills had a plan to bring in lots more of themselves and take over whole populations, so it is entirely possible that massive numbers of people on captured worlds will become hosts for the Bluegills (enough to create the need for the Federation to attack whole worlds, perhaps not so much that you cannot have a 'resistance style' campaign on these worlds). How fast can something like this spread? How much "coverage" can it get? These are some key questions to ask. Be sure to make the bluegills take on new tactics: a different placement which is not so easily detected perhaps or a strain of genetically modified Bluegills specially modifed to take over Starfleet (which after all is going to check right off for the purely physical signs after their little problem in "Conspiracy").
It may or may not be TNG-style Trek (maybe DS9 style would be closer), but hey, it's your game and a darned good idea too. What more heart-rending thing can happen than a crew of Bluegill-controlled officers attacking your ship? Every casualty you inflict, every victory you take from the 'enemy' is a living nightmare. It could practically paralyze any sane leadership trying to fight against them, which in fact is used by the Bluegills. New weapons might be developed such as a refinement of the energy draining weapon of the Breen (perhaps causing the Crew to deal with the Breen themselves for the weapon's specifications and other unsavory aliens to modify it) but until then you have to blow up your Bluegill-controlled opponents in ship-to-ship combat. What about loved ones? The Dependent disadvantage becomes really important once you find out they have been taken over by a Parasite
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- Alice Roosevelt Longworth