As far as you know, the revival stuck to one of its initial plans—starting and ending with
mythology chapters—but the hours in-between were shuffled. What was
filmed as Episode 2 is now running as Episode 4; what was filmed as
Episode 4 is now airing as Episode 5; and what was filmed as Episode 5
aired as Episode 2.
Though fans might be tempted to blame higher-ups for tinkering with the airing order, The X-Files
creator Chris Carter says the shuffle was done to tell the best story
possible. “Because we have a story arc that runs through the middle of
the series…we were concerned that, coming right off a mythology episode
[and] going right into a standalone episode, people would say, ‘What’s
happened?’” he explains. “So, it actually worked out. It served Episode 2
better to replace it with 5. It created a better continuity.”
While the revival’s flow might change slightly with the reordering,
“we’ve come and done what we’ve always done: we give you an amazing mix
of episodes—we’ve given you thriller episodes, we’ve given you scary
episodes, emotional episodes, comedy episodes,” Carter says.
Since Mulder (David Duchovny) and Scully’s (Gillian Anderson) first
days back on the X-Files are now airing as the final standalone of the
revival, Carter acknowledges he had to cut out “a sliver” of the episode
to make it fit, continuity-wise. “It’s not even a deleted scene,” he
says. “It was lines of dialogue.”