Okay, X-Files News Dot Com has the latest batch of set photos and, in the pictures, Mulder has a beard. Why does Mulder have a beard? Well, let's ruminate, shall we?
I've been thinking a lot about the strange situation "The Truth" left Mulder and Scully in and how it will be reflected in the movie. Chris Carter is faced with three major status quo problems going into this movie:
1) Mulder and Scully are a couple.
2) Mulder and Scully have a child.
3) Mulder and Scully are on the run from the government.
All these of these situations will need to be fixed. Carter isn't going to want ANY of those plot points to exist in the movie. He going to want a non-romantically linked Mulder and Scully working for the government investigating cases, without having to mention the babysitter watching little William back home.
So this is what I think is going to have happened between "The Truth" and "Done One".
Baby William will have died, perhaps because of the difficulties of life underground and on the run. The death of their child is too much for the couple, and Mulder and Scully break-up. (There's two of the three problems fixed right there.)
Following the break-up, Scully returns to the mainstream government work, only to discover that there has been a change in regimes and she and Mulder are no longer wanted criminals. Scully spends years working as part of the system, while Mulder refuses to trust the system and remains underground.
They don't speak for years. Scully works to make a name for herself and a respectable sicentist and distances herself from her past on the X-Files.
Then, Scully gets involved in a case that can only be described as 'paranormal'. She's in over her head and needs help. She is forced to seek out her old lover, her old partner, her old friend Fox Mulder.
Mulder's been living as a bearded, crazy underground paranormal researcher, but without the resources of the FBI too aid him and without the scientific knowledge of his old partner, he hasn't accomplished much.
Scully finds him and convinces him to return to the fold. He shaves his beard, puts on the old suit and they head out to investigate this X-File together for the first time in five years.
All of our problems are solved. We have a non-romantically linked and babyless non-wanted Mulder and Scully working for the government and investigating the paranormal together, without all of the baggage of the last two seasons.
I'd been thinking about this for a while and seeing Mulder in that beard only convinced me further that this is the approach they are going to take.