Um...Babylon, methinks the use of existing organisations won't appeal to many people. After all, everyone has a view on politics.
Compromise, of sorts, but must be using alternate timeline:
After centuries of mistrust and paranoia, the current technologically advanced (mainly due to so-called 'self-preparation') world is now moving into a modernised order.
A pact is created by many major powers to try and stem the backstabbing.
But like our world, the ‘east and west’ conflict is true, and other major powers will hate this idea. A Rogue Government who hates the new world idea (no reason given) decides the best way to gain is by joining the pact, but (secretly) only for their own gain. They eventually hold very important placings within the pact, or at least have bribed particulars.
They have done this so that they can ‘suggest’ an initiative (see earlier post) to “help the world along the way to this ‘new world order’” and that this initiative will soon be theirs to control (behind the shadows again), and if the true experimentation is found out, the pact will shatter from the extreme mistrust that will follow.
Two birds with one stone: the experimentation (may need to revise) and to kill the pact which they have hated since its -with them emerging as the political winners afterwards, the experiments giving them ultimate unchallengeable control.
I think for this version to work, a less ‘dark force’ themed Source may be in need.
So, effectively a slightly different but darker conspiracy, but I quite like it.
Now here is the interesting bit. If the player finds out about the source in the first game and the conspiracy later...
In the first game, they would have the opinion that the information is to be told to the world for its own good.
In the second though, the outcome of this would be so different that the player’s stance would change greatly, and different action would be needed. (Because if they did tell, the pact would come crashing down anyway, and the world would settle into carnage. Maybe the player might never get the word out, just leaving the Rogue to suddenly realise that all their research was ruined, and the decades of work was wasted. What else could they do? Nothing, and the pact would be safe. Maybe like Covert Front the player disappears for their own safety, and to keep the information safe forever.)
Whoopsadaisy. 
