Waaaait. It has been a really (really) long time, so I might be totally wrong, but is it possible that the first X-Files movie takes place between these 2 seasons? I remember Scully standing on the beach and the reveal of the alien ship leading into the movie!

I really could be wrong, though. I got to a point with X-Files where I would instantly forget mytharc episodes because I just didn't have any more room in my brain. The standalone episodes, I remember clearly and fondly, but ask me about the overarching plot and I have no idea.