This takes place during The Goldberg Variation with references to The Sixth Exctinction II: Amor Fati
Implications
"Hey, nice outfit"? "Hey, nice outfit"? Seriously? Scully was sure that, in 7 years of partnership, it had been the first time Mulder ever commented on her outfit. Certainly with that kind of look.
Deep down Scully knew that something shifted a bit in their relationship since that near kiss in his hallway a couple of years ago, but here, since the Millennium, something shifted big time, and now, she did not know how to respond to that.
She and Mulder had a very deep bond. Always had. Hell, they went through so much together that this bond was probably unbreakable at this point. The thing was, their mutual trust went so much beyond what she ever felt and experienced before, that she still was not sure of the nature of that bond. It kind of always remained a mystery. The way it formed. The way it evolved itself almost as if it was a separate entity.
Since he kissed her, Mulder was different and she really started to wonder if he wasn't trying to seriously initiate something other than friendship. She was starting to think that Mulder really had feelings for her, after all. Diana made her seriously doubt that what happened in the hallway had been something significant for him. However, Diana was now dead and if Mulder's latest monologue about her being his touchstone had been any indication, his feelings were pretty serious.
If she was honest with herself, she too, had feelings for him. Only she never really had taken the time to think about those. It was a territory that she swore to herself she would never come back to. She could have had thought about the near kiss in his hallway or this night playing baseball with him, but she had decided against it. Mulder was her friend and her partner and she had been determined to make the best of this. Even when he told her he loved her, she had not responded. Conveniently taking it as a drugged infused confession, she just remained loyal by his side, as if nothing had happened, not willing to think about the implications of all of these moments.
At that time, she thought it had been the best thing to do, especially after what happened with Diana.
Scully was a very rational creature. She believed this was the main reason why she did not do spontaneous. She really believed experience and rationality should prevail on instinct and emotions. Only, if she was really honest with herself, Mulder had made her a bit more naturally spontaneous. She even openly initiated a flirt with him not so long ago. Adding to that what he told her that morning, when she came to tell him Diana had died and those kisses they shared, Scully found herself at a loss about what to do now. Perhaps it was time to think about those implications, after all.