Watched the next part of the Mythological arc last night and while it was good, I don't think it was as great as the arc that opened the season. It was nice to know where they took Scully during the Abduction, but I was a little disappointed that the whole Alien Abduction was a smokescreen (Or so this episode told us) and it kind of brings us back to the theme of season 1 of if you believe in something so strongly, the things you witness might just be scenes you want to see or they want you to see. That's pretty much what these episodes are. Mulder sees what looks like Aliens and they are only just lepers that were part of the WWII experiment. These episodes kind of served as another story in the whole Alien thing, and not getting everything so quickly.
I did like X in these episodes though. Maybe it was we finally got to see him do something, weather it was telling Mulder not to board the train or saving Mulder at the end.
Overall, I'm not saying these episodes were bad, because they were very good, but it almost felt like misdirection and another layer to this arc which is already pretty big.