The paragraph describing Scully's first sight of the Doctor.
The scene that runs from Scully's line, "I'm afraid you're going to have to come with us," to Mulder's "But I think we have ourselves a consultant on this case."
From Mulder's "It's a police box," to Scully's "What's it doing here?"
When Scully gets out the UNIT fax, the dialog from her line "This Doctor seems to have been .." to Mulder's "... paid unscientific advisor?"
From "I think he's a time traveler" to "I think he's here to shut it down" - except for from "Time travel's impossible." to "Or a 'relative dimensional field', whatever that is." These two lines referencing Scully's thesis were added to the scene after the airing of the fourth-season X-FILES episode that dealt with time travel.
The dialog between Cancer Man and the Brigadier.
From "Mulder waited for the Doctor ..." through the Doctor's line "whether it was true or not".
From the Doctor's line "It's difficult to backtrack ..." to the Doctor's line "I mustn't say any more."
The entire plot element of the Doctor suppressing Scully and Mulder's memories at the end was added after the X-FILES episode about time travel was aired. The air episode made it apparent that Mulder and Scully had never discussed the possibilty of time travel between themselves, at least not that they remembered, previous to this episode's events (my story is set early in their recorded history, allowing for the possibility of more such crossovers).
Once arrived at, this plot element allowed Scully to participate in the action, instead of it being hidden from her so her skepticism might be preserved. It allowed the opportunity to fire her skepticism up and then temper it with an appropriate, if subconscious, tolerance, early in her relationship with Mulder. All this makes Scully the hero of the story in the Campbellian sense, and this makes the story a genuine X-FILES story, instead of just a DOCTOR WHO story in which the Doctor's companions happen to be F.B.I. agents named Mulder and Scully. (Since the Doctor is such a fantastic and fantastically charismatic character, it's a real danger in crossovers that he will overshadow his fellow hero[es] so much as to defeat the purpose of writing a crossover in the first place.) And finally, this plot element gave the story a very nice last scene and last line.
Such be the pitfalls and joys of writing in a shared universe, or in more than one at once.
One last note:
When originally posted to Usenet this story was dated as 1992, on the basis of data from a work entitled THE UNOFFICIAL X-FILES COMPANION. In the absence of "official" information, however (which isn't to say that I know whether it actually exists), I prefer to assume that events depicted on THE X-FILES, which began airing in 1993, occurred in at least the same year as they were aired. After a recent viewing of the X-FILES pilot and series premiere I have discovered that its legends do set it in March of 1992. But in compromise I had already excised all references to year in the date headers in the story, which is anyway how they usually appear in the legends on THE X-FILES these days.
Less-than-Total Recall, a short-short sequel to this story.
The DOCTOR WHO/THE PRISONER crossover referenced by the Doctor's dialog in Chapter Five
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