Strange fact.
It's been a long time since I've played IW, and I've just finished DX again today. As far as I remember, in IW it is assumed that you merged with Helios AND destroyed Area 51. That is plausible, because after you merge with Helios JC still has the fate of Area 51 in his (and Helios') hands. However there is an inconsistency here: Why would Helios destroy the Aquinas Hub? Why would it hamper its own ability to see the content of every single electronic communication message around the world?
Well, that's not my point. The thing is, in Area 51, just before you see Bob Page for the first time, there are a few containment vats, for supposed clones. You see JC Denton's name in one of them, so it is assumed that it's where he was born. I automatically assumed that Alex Denton from IW was the clone in the other vat, labeled "Alex Denton".
There comes the problem: In order to achieve the "Dark Age" plot development, it IS necessary that JC, at some point, blows up Area 51. So how come you are playing Alex Denton in IW? How didn't he get destroyed along with Bob Page, Area 51, Aquinas Hub, and everything else? Is it possible that JC/Helios deliberately awakened Alex, to use him to achieve his own goals? If so, what implications would this have on IW's storyline?