Maybe they'll do it like "Seinfeld" did it with George Steinbrenner, have Mulder be seen ony from behind.
I wonder the same thing, I hope they find a reasonably good way of explaining it.
/Mike
Quite simply, he's no longer employed at the FBI and therefore has no claim to the X-Files. He'll probably be out on his own invetigations, but the show will only focus on the offical FBI ones with Scully and Doggett (and the new chick who's character name escapes me).
My guess is they will say he had to take a job out of town, or is out of town looking for work. Having Scully in jeapordy without Mulder there will require some sort of cover story.
Expect a shot or two of Scully on the phone telling "Mulder" that everything is OK and not to worry.
they WON'T make Mulder a deadbeat dad. that much i can assure you. more than likely he will have gone off to track down a lead on something. his name will still be mentioned quite a bit this season because believe it or not they still do want to do the next movie and Mulder will most surely be in it as a major player.