In spite of all the tonal inconsistencies, I liked the episode until the final segment. Scully referencing Mulder's first words to her from the Pilot was cute, and Mulder's mushroom trip sequence was legendary. I was rolling!
But seriously, the last 10 minutes or so was complete dog shit. Carter's "final word" illustrated through the last two conversations was so heavy-handed, and unearned based on the preceding 30 minutes (which were largely comedic)
This is the fourth episode now that has been notably hampered by the six-episode format. The last movie tried to tell too many different stories and explore too many themes, to the point where nothing was allowed room to develop naturally, and instead everything felt forced and half-baked.
Same thing has happened here. The premiere tried to cram in so much in 42 minutes that it was a complete train wreck. "Home Again" tried to tell two stories in one (with the MOTW aspect being relegated to the background), and the "treating people like trash" thread connecting the two felt tenuous at-best. And then this week, again, it felt like Carter had at least two ideas but only one episode to work with. So instead of executing on one of those ideas well, he stuffed them both into the same episode, and it just never came close to working.
Only Darin Morgan's episode was a true standalone, and it's no coincidence that it's far-and-away the strongest of the five. I applaud him for just trying to write a good X-Files episode, and for not trying to shoehorn every idea in his head into one jumbled mess of an episode.