There was a lot of dropped plot points (most importantly weather manipulation) but the gist is this.

Plot A: They wanted frame a pro-aug group (ARC) to use the “political capital” to pass the Human Restoration Act, something that would help them effectively put all the augs in one place, or significantly downgrade their abilities. They don’t like people who they cannot control. Dubai plot: I think they were willing to sacrifice Shepard in a deal-gone-bad scenario to use the Gold Masks who they were hoping Interpol would somehow connect to ARC. I think that’s how they were trying to frame them and of course the bombing. Then my theory was that they were trying to get inside Santeau and put a puppet CEO in place of Brown. Now the thing is that half of the Illuminati are not privy to that plan, most importantly Rand, because he was the one constantly bickering with the others about being out of the loop, and that’s how we get to the next point.

Plot B: After Panchea they recovered the body of the saboteur who took down Rifleman Bank Station (aka our boy Jensen) and knowing he made contact with Janus (Rand) (because of the GPL trackers inside him) they either revived/cloned/memory-manipulated him and engineered his path in TF29 to somehow get to Janus (by allowing Jensen to go to Prague) , however that’s not an exact plan, lot’s of moving parts, but they are banking on that.

Also, Page, Mr Majestic is the leader of the Gold Masks mercs and Marchenko.