In an interview with Sci Fi Wire, David Duchovny said that he won't be returning in the ninth season of The X-Files, even in a small way. While speaking to the press while promoting his upcoming film, Evolution, Duchovny said that he would not be doing cameo appearances as he had in the last season.

"I don't think that's fair to me or the fans and I'll tell you why," Duchovny said. "I think that the consciousness of the show is this quest of Mulder's, and the core of the show is Mulder and Scully. When I came back at the end of this year, by necessity and by my choice of not being on the show full-time, other ideas, other stories, had to come center stage. When I came back, I felt somewhat peripheral. Not me, but Mulder's story was somewhat one of three or four stories now that were going on. It didn't feel like the same show to me, and I think to bring back Mulder peripherally is not fair to the character that I feel a lot of affinity for. I feel like the fans respect Mulder as the center consciousness of the show, and to have him come back, like Superman's dad or whatever, just feels cheap to me." However, Duchovny said he would still be interested in another X-Files feature film.

As for questions left unanswered at the end of the last season, Duchovny said he did not know who fathered Scully's child, nor how the season finale's ending kiss would resolve next season. "I will be interested to see, like anyone who is a fan of the show, how it gets resolved, because they will have to resolve me while I'm not there. I hope they don't say, 'Oh, I'm glad Mulder's gone. What an ass--. He had a baby with me, kissed me and now he left.'"