This second half of the episode named 'my struggle', a name that now makes sense. It is also the last episode of the season (que disappointed 'aaw' sounds). It starts with a monologue by Scully, mirroring the monologue by Mulder in the first half. Of course, Scully monologueing has more history on the show, what with her reports often wrapping up an episode and all.
Einstein and Miller (Faux Mulder and Phony Scully) are back as well. The episode could have done without them. Einstein at least has something to do (helping real Scully), though that role could have been better fleshed out if filled by the nurse we've come to known. Miller, for most of the episode, only seems to be present to show the audience he still exists, before being awkwardly shoehorned into the plot. Monica Reyes makes an appearance, which is only interesting to the most hardcore of fans, since she is one of those later season characters. Like T-1000.
The overall plot, however, is great. It really ties the show together. The main conflict kind of reminds me of 1989's Batman, which is always a plus. One notable difference is the scale, X-Flies amps it up to a global level. The ending is surprisingly open, hinting at the possibility of more to come. I certainly hope so, because watching the past six episodes have been a blast. Still, it does feel somewhat unresolved. For an episode that so neatly ties up older loose ends, it also creates a few.