He's a plant by A.D. Kersch to debunk the X-Files once and for all. Of course, he sees the light, boinks with Scully and will take over for David Duchovny in the future XF movies (just kidding on my second sentence).
I'm interested in how they're going to explain Scully's pregnancy. Rumor on some of the XF mailing lists is there's some footage of Scully and Mulder in a clinch that was supposed to air last year and got cut, but will air in sort of flashback mode this season to explain it all. It's better than the alternative - I don't think I could stomach another alien pregancy storyline.
When I first saw the T2 guy was going to be on the show, I wasn't sure he'd work, but after seeing some of the previews, I'm pleasantly surprised.