Mulder is about to pummel Padgett because he’s jealous that this guy has come on to Scully and she’s responded to Padgett’s interest in her. However, Padgett notices that this slight touch by Scully to Mulder’s forearm stops him in his tracks; this is the power that Scully has over Mulder. Scully knows Mulder’s a little jealous of Padgett, so she touches him to indicate she knows what’s he’s up to and to stop it. Just by the facial reaction from Padgett, he realizes the powerful connection between Mulder and Scully.
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“I think what makes the relationship between Scully and Mulder sexy is the respect they have for one another. It’s that tension. We’ve done some incredibly intimate scenes that have nothing to do with sex. Beginnings of relationships are always the most exciting - that period when you’re courting and you get near each other and start breathing heavily. The hottest stuff is before you ever touch the other person. Or the first touch. So Mulder and Scully’s first touch in an episode or first touch in many episodes becomes more exciting.”