From the Gillian Anderson Fan Site:

Frank Spotnitz, the mastermind behind much of the mythology of The X-Files, told SCI FI Wire that he has signed on to help write the next movie based on the hit series, but that the new movie won't deal with the show's byzantine conspiracy arc. "There's still a very good chance that we will all do another X-Files movie," Spotnitz said in an interview. Spotnitz was an executive producer on the show, which starred David Duchovny and Gillian Anderson; it ended its nine-year run in 2002.

One point of contention in getting a second X-Files film off the ground: Series creator Chris Carter is still wrangling with 20th Century Fox over legal matters. "David, Gillian and I, and even Chris Carter, all have deals in place, and once the legal issues are over with, we will go on with it," Spotnitz said. "I'm hoping it will get resolved soon."

Although the script isn't written, the idea is already developed, Spotnitz said. He added that Fox likes the idea, which harkens back to the series' stand-alone episodes rather than the conspiracy to cover up the existence of extra-terrestrials, which was the subject of the first X-Files movie.

"No, we're not going into the mythology [in the sequel]," Spotnitz said. "One of the things that was exciting about doing it is to not make it a mythology story, and it's like one of the stand-alone episodes. It's a bit scary. Of course, we will catch up with the characters and what is going on in their lives, but it's not about the alien conspiracy. It's not about that." The first X-Files movie came out in 1998.