According to Fox Chairman Tom Rothman,X-Files 3 may be made.Here's the excerpt from a recent (10/2008) interview with IESB.net:
"IESB: X-Files, truthfully, I'm a huge X-Files fan, I was a bit disappointed with the new film. It didn't feel like an X-Files movie, but I hope to god, I know there's an idea that Chris [Carter] had about the 2012 mythology of the X-Files, the alien colonization, any chance we'll see X-Files 3?
TR: It's really up to Chris, David [Duchovny] and Gillian [Anderson].
IESB: The second one wasn't an expensive film.
TR: No, but it wasn't a matter of the money, that was the film that Chris wanted to do. He was determined to do a stand alone film, a film that wasn't dependent upon the mythology. His interest in making the movie, was in the characters and in their relationship, not the mythology."
