The first meeting was coupled with anticipation and suspicion each knowing that the other was there to disprove Mulder's work. As they grew more comfortable and Scully saw things that science could not explain they began to develop a trust between them. Two episodes in general come to mind in which there were Sparks. Beyond the Sea and E.B.E. There are more much more coming so be patient.
In Beyond the Sea the first spark is struck in there office when Mulder says he is sorry about her father. He reaches out lightly strokes her cheek, holds his hand there and looks at her with that patented concerned, but hiding bigger Mulder feelings that he is know for. Abbreviated C.B.H.B.M.F.L . At the end in the hospital Mulder lightly puts his hand on Scully's shoulder and gazes ( which he would deny vehemently) at her respectfully.
In EBE, there were no big sparks, just two I could see. First after Scully meets the Lone Gunmen, and is discussing them back at the office; Mulder says " I think it is remotely plausible that someone might think your hot." Scully does a quick double take, blushing continues talking. Second, after Mulder confesses Deep throat lied to them, Scully says, " Your the only one I trust". There was a brief pause and shared gaze.
Mulder is very protective this Season. He takes on the father role left vacant by Scully's Father's death. He realizes she is vunerable and needs support. He realizes that their budding friendship fills a hole in his own life created by the nature of his work. Ok maybe that last part was a stretch for this season, but it never hurts to try.
Squeeze
This episode was the third of the series and a good one it was. The mulder glasses reappeared always a good sign and Mulder coined perfect flirty phrase with "Do you think I'm spooky?"
There lots of good double entendres?? here.
" It seemd like you were acting very territorial."
" Of course I was." Mulder says reaching out and plying with her necklace then letting it drop but occasionally fiddling with it, Scully looks confused at first then flattered. Getting his double meaning. he was territorial over her as well as the x-files. Then he elaborates on his territoriality of her by saying,
" In our investigaions, you may not always agree with me but at least you respect the journey and if you wnt ot continue working with them, I won't hold it against you." he was trying to allow her a normal life with that last statement, but she rejected it in order to remain with him
Then anohter good Mulder line came into play more funny than sparky
" Is there any way I can get it off my fingers quickly with out betraying my cool exterior."
Tooms