Four pages survived both drafts intact and never reached the screen.
White pp.11–14 · Blue, unchanged · never aired
Scully arrives at her mother’s house in the middle of the night, having walked there, and breaks down. On the disc that scene ends where you would expect a scene to end:
AIRED — 08:06–08:22
“What is it, Dana?” / “I’ve made a terrible mistake. Dad would be so ashamed of me.” — sobbing — then Albert Hosteen’s narration, New Mexico, morning.
In both drafts it does not end there. Scene 15 gives way to Scene 16, a long sequence in the living room afterwards: Scully with her legs up on the couch, her mother talking her down, and then Melissa coming through the front door. It runs from script page 11 to page 14 and it is the only extended conversation Scully has with her family in the episode.
WHITE (07/03) & BLUE (07/12), SC.16 — NOT ON THE DISC
MRS. SCULLY: How can you fault yourself, Dana? You had to make a choice. I think you did what you felt was right. SCULLY: No. I did what I felt was right for my partner. MRS. SCULLY: But wouldn’t Mulder have done the same for you? SCULLY: Yes. But that’s just it. I behaved exactly how Mulder would have behaved. I lied and countermanded my superiors because the pursuit of the truth seemed more important.
Her mother’s answer to it is the thing the broadcast most conspicuously loses — a direct reply to “Dad would be so ashamed of me,” which on air is left standing:
WHITE & BLUE, SC.16 — NOT ON THE DISC
MRS. SCULLY: Dana. If you’re really worried about what Dad would have thought of you — I think he would have seen there was no right choice. Or no wrong one. (Dana does not appear heartened by this.) I think he would have been proud and supportive of his daughter either way.
same scene · both drafts · never aired
The back half of Scene 16 is a two-hander between Dana and Melissa, and it is the episode’s only real Mulder-and-Scully material — conducted, since he is nine hundred miles away in a hogan, entirely in the third person.
WHITE & BLUE, SC.16 — NOT ON THE DISC
MELISSA: Something’s happened to the man you work with, hasn’t it? … I’ve been feeling it for the past two days. SCULLY: Melissa… Mulder is very likely dead. MELISSA: You don’t believe that. SCULLY: No, I do believe it, Melissa. MELISSA: Well, I’m getting strong feelings otherwise. SCULLY: I wish it weren’t true. MELISSA: No, it’s deeper than that. You’re radiating, Dana. You have a connection with him that is still strong and powerful.
It escalates into a real fight. Scully gets off the sofa “angered by her sister’s loopy insensitivity”; Melissa tells her to get a second opinion; Scully tells her this is not a medical condition but a statement of fact, and that based on the empirical evidence — “which I happen to have gathered” — it looks like a pretty damn sure bet that “you’re whistling in the graveyard.” Melissa answers that if she could see through her guilt and anger she might look past her Western empiricism. And Scully ends it:
WHITE & BLUE, SC.16, LAST LINES — NOT ON THE DISC
SCULLY: Thank you. I’ll make sure to consult my tarot cards when I’m out looking for a new job. (beat) I’ve lost someone, Melissa. I’d like to deal with it in my own way.
Both drafts hold it word for word; the Blue does not mark a single line of it. Whatever removed it happened after 12 July, on a stage or in an edit suite, and it took with it the only occasion in the episode on which anyone says out loud what Mulder is to her. Melissa is shot in Scully’s apartment at the end of “The Blessing Way”; her death follows in “Paper Clip.”