David Duchovny has been talking about the possible plot of the X-Files 3:

X-Files 3 Movie

“As far as the X-Files movie I’d like to do next, if we get a chance to do it, would be a return to the heart and soul of the mythology, which is the alien-oriented conspiracy. I think it’s natural for The X-Files to have another movie in 2012, so we’ll see if we get to do it.”

Actor David Duchovny

So he’s confirming what Director and Scriptwriter Frank Spotnitz said. So yes we can be confident that the aliens and the conspiracy will be the central theme of the movie X-Files 3. And I think they’re going to release it in 2012 so to stick to the series mythology. All in all, that’s good news!
:)