You know, the first time I watched IWTB I was afraid of the same implication you observed, but the second time I watched it - even without the post-credit shot of the two of them happily on vacation - I concluded the exact opposite. She was in turmoil over the procedures she was putting her young patient through, and that's what was so hard on her; not her relationship with Mulder. She was leaving to perform another surgery on the boy, when Mulder offered to take her away from it all, and when she said, "Don't make this harder than it already is," I took it to clearly mean she was just finding it really tempting but knew she couldn't cancel the surgery, not matter how hard she was finding it to "put the boy through hell" (as another doctor and then Scully herself had put it).
I suppose it's still up for interpretation (in the true spirit of the X-Files...), but that's how I like to see it, anyway. XD
I saw one fan say she kind of liked how Scully threatened to break up with him because if they can break up, it makes them a real couple.
And yes, I read about the possibility of XF3, and I am so hoping it happens!
Julie
