In a recent interview with Empire Magazine, Chris Carter mentioned that he has a story for a new X-Files movie ready to go, and he's just waiting for a green light from Twentieth Century Fox to get going on the project.
It's really up to Twentieth Century Fox, whether they have the will to do it. I think all of us are interested in putting the band back together. I have an idea for a third movie in my head. The colonisation date has passed and that is something we wouldn't ignore. For the second movie, we only had the budget for a standalone story, but we want to go back to the mythology.
He also mentioned that he wanted to get Simon Pegg for I Want to Believe but didn't have a part that would be the right fit for him, so if he got the chance to do a third film, he would definitely look into including him.
Considering how much rich history and dangling plot threads are left for another entry into the X-Files collection, it's good to see that Carter would be interested in going back to the roots of what made the X-Files a great show instead of doing another standalone/throwaway storyline that was found in the piece of crap that was the last movie. Hopefully the forces that be will get on board with the project and allow us to see what takes place next.