That seems to be what would be indicated by the spoilerific spy pic below, snapped by a sure-to-be-in-trouble-soon photographer near the Vancouver set of X-Files 2, and sent in yesterday to JoBlo.com:
That's creator/director Chris Carter on the right surveying the special effects handiwork. I was never that into X-Files, but I do recall there was a lycanthropy-themed episode or two during the show's original 1990s run. If that is the direction in which Carter is going, there are going to be a lot of X-heads plenty upset that there will be no continuation/resolution of the epic alien invasion saga, I can tell you that.