Phlogiston is what 18th century chemists thought made up cumbustion (or the stuff of a flame) and what was in combustible bodies, and to be released in combustion.  I could see these being living in stars, with the ability to survive the gravity and intense heat.  I would give them a flame/fire/plasma/ash motiff to represent their hot nature.  Their main feature is the ability to colonize stars, and start with a colonized star (sets home planet).  Their tech tree would involve features that let them manupilate the stellar output of their stars (this would be similiar to the planet depletion effect), increasing FIDS for all other colonized planets in that system.  This would also allow them to burn out stars which is their main goal, as burned out stars is their ideal world, and their goal is to dim all stars in the galaxy.  They would have benifets on (or start with) gas giant colonization, and could maybe have the ability to manipulate the unconlonizable systems (proto-star, collapsing star, etc) and either have those system be colonizable, or in some way to accelerate (proto-star) or reverse (collapsing star) back to colonizable systems.  For their "spy" aspect allow them to colonize the suns of other empires, allowing them to be unnoticed gathering intelligence (system awarness), but also if friendly with that empire, build ships and other stuff as part of a limited build list.  

So in short, Phlogiston (or Phlogistan), the peaple called the Phlo (like Flow).

I think this would be a fun way to add new features and concepts to the game and to custom factions, and to respect what some of our ealiest scientist thought made up the universe.