Scully is not just in, she is

'Leonard Betts' told us that Scully has cancer and, thanks to a shuffling of the production order, 'Never Again' showed us her reaction to that news with an uncharacteristic night of near passion. In 'Memento Mori' we finally see Scully begin an attempt to fight what she terms "science's demon possession".
That she does so designate her cancer in this way is rather telling for it shows the extent to which she has become immersed in Mulder's worldview. This is little less than shocking coming so soon after the near break-down of their relationship in 'Never Again'. In that episode, Mulder made the distinction between them clear:
But let me remind you that I worked my ass off to get the files reopened. You were just assigned. This work is my life.
Scully does respond that it also becoming hers, but Mulder is right when he retorts, "You don't want it to be."
Even after all the pair have been through together, it is not unfair of Mulder to recognize this difference. Scully was assigned to the X Files and to 'debunk' them no less. True she has grown to see the value of Mulder and his crusade, allowing herself to come to a belief in a conspiracy, yet it remains for her more a job, a vastly important one involving national security and the saving of humanity from alien hegemony, but a job nevertheless.
This distinction is to be seen in 'Never Again' when Scully complains,
I feel like I’ve lost sight of myself, Mulder. It’s hard to see, let alone find in the darkness of covert locations.
While it is not unreasonable for Scully to want a life, she reveals her distinction to Mulder who sees no life for himself beyond the X Files. For Mulder, the X Files are his life. They are not Scully's.
Until 'Memento Mori'.
Scully has always been reluctant to accept what happened to her in Season Two's 'Duane Barry'/'Ascension' two-parter. Even in 'Memento Mori' she apologises to Penny Northern for not sharing 'those memories'. In the very next scene, however, on the phone to Mulder asking him to bring the "overnight bag from the trunk of the car and I need you to call my mother and ask her to bring up some things at the hospital", she admits "I think that we both know that right now the truth is in me". Not a classic line, to be sure, but an important one, it being Scully's acceptance at last of what happened to her.
Mulder is wrong in his judgement of Scully. He is right that there is a clear distinction between them, but he misidentifies it. He comes close, at the end of 'Never Again' when he congratulates Scully "for making a personal appearance in the X Files for a second time". What he doesn't realise is that Scully doesn't just appear in his filing system - Scully is an X File.

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