One of the elements in our latest Battlestar Galactica campaign that would translate easily into almost any modern/future setting is the use of non-profit foundations as a villain organization. It’s a nice change from the tired “evil corporation” trope of cyberpunk, and fits well into the police state fascism of cyberpunk settings, or the world of Firefly, or spy-fi campaigns. These non-profits are generally thought well of because they appear to be honest brokers — they aren’t making money off of their policy positions (not true, of course), they claim political nonpartisanship (not true — in fiction or reality), and often have a wide reach. These groups don’t just target politicians, they get their hooks into education by providing money, and they insinuate themselves into business practices through advocacy.
Here’s a couple of groups that, with a bit of tweaking could be used in any setting:
PROMETHEUS GROUP (Battlestar Galactica version)
This is an umbrella holding trust that controls the money and operation of various non-profit foundations. They have their hooks into policy think tanks (The Prometheus Foundation), educational scholarship funds and advocacy (the Lucan Foundation), and Center for Colonial Progress (a political lobby firm that pushes social programs and funding for the same.) The group and the Lucan Foundation were formed by entrepreneur and former Virgoninan politician Count Azarius Lucan. The count is now a reclusive figure, pulling the strings after a near-fatal accident while orbital skydiving. He suffered extensive surgeries following his accident that could have allowed the Cylons to either replace him, or alter him in some way to be their master agent on Virgon.
It should be obvious how this can be tweaked for usage in any futuristic game that involves cybernetics, cloning, or even psionic manipulation. Lucan (I’d change his first name for modern settings) is a quasi-tragic figure — the former scion of whatever policies the GM’s universe deems “good” turned bad guy because of outside influence. (Better is he was always a bad guy, but he hides it well; sort of what they were going for with Dominic Greene in Quantum of Solace, but tip their hat too early.)
For a modern setting, you could just use real foundations as your bad guys; they are legion, but the Prometheus Group could be some kind of international group manipulating politics, terrorists, businesses, to create a world (dis)order that benefits them monetarily or politically. It’s world domination without the nuclear blackmail. What makes this sort of black hat organization so insidious isn’t just that they are seen as good guys, but that their monetary influence would extend throughout the political system that controls your police precinct, spy organization, military unit, or whatever — your own people don’t want to see you succeed because of the hit they will take to their funding stream, or it could implicate them in dirty deals, or simply act as an embarrassment during election time. You will be fighting both the villains and your own command structure.