That was the Wiseman's Committee/the Philosophers, wasn't it?
That was kept relatively secretive in the sequels. They didn't go into every minute detail like they did with the Patriots.
Yeah, if memory serves, the Philosophers were presumed to be behind the events of MGS2, but the post-credits scene revealed that they had all been dead for over a century, so it was either a different secret society, or some sentient AI fuckery. It actually tuned out to be both...