Deus Ex consistency

So... Bob page left Morgan Everett's wing to fund MJ-12, because morgan wouldn't let him have much say on the illuminati's decisions.
But, at the start of DE:HR, we see him have a conference with the illuminati members.
Care to explain?

DE:HR has a lot of plot holes in regard to Deus Ex as a whole. For example, it's meant to be, what 25 years before Deus Ex 1? But there are emails from Nicolette DuClair in the game when she wouldn't even be born.