What if the Ordo Veritatis from 'The Esoterrorists' were a subset of one of the branches of the illuminati, AND were part of CYCLOPS? Just the right blend of Shadowy Conspiracy, Red Tape Aiding The Apocalypse, and Corrupt Field Operatives Save The World. Could easily be used as...
1- Antagonists who sometimes show up and help against a common threat.
2- The PC's employers.
3- The group that puts explosive collars on the PCs after a TPK type event, to allow further adventures instead of just starting over from scratch.