Deus Ex: MJ-12
Comments(0) Deus Ex is impressively thorough about name-checking popular conspiracy theories and secret societies. Area 51, Majestic 12, the Knights Templar, the previously noted Trilateral Commission, and so forth. One bit-part NPC even asked me if I knew the widow’s son. (Do the freemasons even count as a secret society any more? I’ve seen them advertise on television, for crying out loud.) There haven’t been any references to the Kennedy assassination yet, but I’ll be surprised if the game ends without mentioning it at least once.
I assume that not all of these references will be concretized in the actual story. Many NPCs just have their own little paranoid suppositions, usually based on mistrust of privilege. Which is to say, they’re broadly correct, but they have no real basis for the details. Theories of this sort can contradict each other wildly. Nonetheless, some of them are already coming true. 
MJ-12 is definitely operating secret laboratories in the sewers, studying the plague. They even have guards with a little “XII” logo on their helmets.
The MJ12 guards are the first enemies I’ve encountered other than the NSF. I suppose I could have used this as an excuse to become more violent: just because I have a rule against murdering the NSF doesn’t mean the same applies to these guys and their clandestine medical experiments on unwilling subjects. But then, the people performing those experiments aren’t the ones shooting at me. The guards are just freelance security personnel who don’t know a thing about what they’re defending; the only scientist present at the site is in fact the guy I went in there to rescue, and as much a prisoner as the experimental subjects.
This is something the game keeps doing: pulling the good-guys-vs-bad-guys rug out from under the player. For example, at another point, a friendly NPC tells me that I’ll need a key currently in the possession of an NSF officer encamped nearby, and that the only way I’ll get it is if I kill said officer. But when I confront him, he immediately surrenders. He’s not even a soldier, it turns out. He’s the company’s accountant.
At any rate, MJ-12 is associated with UFOs, so their interest in the “grey plague”, and in particular their interest in seeing it “fully bond with a human host”, has obvious implications about the plague’s origins. I suppose this is why, immediately after granting me this much understanding of what was going on, the game started throwing Templar references at me. Just to make sure I knew that I didn’t really understand anything yet.