You say "creepy sexual harassment of the girl he raped zero times," I say: He is not talking about Jenny at all.
Chuck continues to encourage her to bag Nate, without regard to Serena's return, and then realizing she probably thinks they can't have this conversation, tosses out the old "I probably won't remember this conversation anyway." Given token permission to explore the topic now, Jenny digs in and before long, they've arrived at a plan to Desdemona that shit using this Hugo Boss shirt. If Chuck can't have Blair, obviously he wants Nate instead. But between Nate's anger at the prostituting, and Serena's intoxicating existence, a bunch of things need to change at once, which means shit-stirring. And now that Jenny's back from Brooklyn, you've got grade-A shit-stirring talent right here. Chaos incarnate! Wind her up and let her go!
Rufus hisses and weaves and lisps at the unflappable Dr. Sandiego until their wife comes home. Lily's moderately pleased to see Rufus, and disturbed by the presence of Wills, but mostly this scene suddenly becomes about Serena, who hasn't seen her father in fourteen years and spent the better part of the summer looking for him under every rock and bridge on the Continent when she wasn't letting yacht-owning Eurotrash drink Belvedere off her tits in Ibiza. Her mouth goes bwuh?; her issues sigh, and finally arise from their disco nap, because it is time to DANCE!
After some Timmy-in-the-well style whining-barks from Rufus, Lily spills the story, which is that every word she's said this entire season has been a lie. "It wasn't my mother who was sick. It was me. And that's why William and I were together last summer. He wasn't treating CeCe. He was treating me." Which, we've pieced that together, fine. But when it gets wicked ridiculous is when the scene starts answering questions we didn't need to discuss, because of how silly it all gets so instantly: "I wanted to see you [Serena], but as her doctor, I couldn't tell you why I was there [in Santorini], and I... I didn't want to lie."
See, because Dr. Sandiego is so dedicated to his medical ethics that he didn't even want to look his daughter in the eye -- as she was going visibly, globally slut-crazy -- on the off chance that she might say, "Hey, I know for a fact you are here on this continent so I just thought we could hang. These hors d'oeuvres are great. So listen, any chance my mother has a mysterious illness that only you know about, or can treat, so she's pretending to be at my grandmother's place in the Hamptons?" And he would have to be like, "Mmm, noooooo. No, that's not what's going on." And that would be a lie. He would have lied.