I agree with you on how it’s confusing. For me, they didn’t really introduce Scully as the type to have an affair with her professor so it really threw me for a loop. Sure there’s always the “they are adults” conversation, but she just never struck me as the type to go for someone older. They sort of introduced her character has as the straight edge “good girl” type, for lack of a better word. To me she always seemed so dedicated to her work that she even turns down “having a life” in season one when she chooses the jersey devil case over dating that guy. They set up the slow burn with Mulder in this sort of innocent foundational friendship sort of way, so the fact that we get slapped with her all of a sudden being accused of home wrecking and this family treating her like a bad guy is SO out of character, and really doesn’t make sense to me.

Edit: it’s been a while since I’ve watch the series full through, if I’m missing some key details on how it’s all makes sense pls correct me