Ahh, okay. I kept hearing people talk about that campaign and had no idea where to find it until this morning (it IS lumped in with the rest of the scenario options or whatever they're called, right?) I'm a couple hours into one now.
Yea, it's not actually an alternate campaign. When it starts it's just a minor faction (which is where it's listed in the lobby), but if you pursue it things change quite a bit. But if you don't, it's basically the same game as without the faction.
