"Jenny, why would you... Why would you do that?" Eric compares it favorably to Damien, but Jenny admits that she didn't do it with Damien. "I wanted to wait. I wanted it to be special." And instead she wasted it on their brother, because she was alone and he was alone, and they wanted to forget, but mostly because Jenny has been doing the same thing, over and over, all season long, and nobody was reacting. Her virginity was for Nate. She knew it, we knew it; he knew it. And because that's the way it had to be, Jenny did what Jenny does: Stepped outside the story, broke it. Smashed the pieces. Hoping somebody would notice and see how far she's gone. Brilliant.
Eric tells Dan to go to their sister, immediately, while Nate arrives to talk to Serena. She breaks up with him, because she honestly thought when Will came back she would stop fucking things up. Nate's sort of disgusted by all this, and tells her if she's out then she's out. And she is out. She kisses him goodbye, and his story falls apart too.
Downstairs, Chuck apologizes to Blair for everything. "I know I can't take it back, but I want to try and make it up to you, even if it takes me the rest of my life." He pulls out an engagement ring, but then Dan arrives for the next big set piece, punching Chuck once again. Blair takes one look at Jenny's ruined face, and figures it all out. The way Jenny just stands there, silently, and Blair falls apart: Gorgeous. Epic. Chuck's sad little face is nothing compared to the unleashing that follows.
"You. Get out of here now. And not just out of this hospital, but off this island. Go and never come back, because if you ever set foot in Manhattan again, I will know. And I will destroy you." Jenny tries to apologize, but Dan points out that it's all about Chuck; it's always been about Chuck. They stand around, with this death curse sort of reverberating in the walls, and Rufus stumbles into the scene yakking about bagel chips before he comes up short, mumbling, "What'd I just walk into?" The first real thing that ever happened to your family. Jenny collapses against her father, and Lily and Rufus take her away. Serena arrives, scared to death by Blair's expression, and Dan takes her away from them. Chuck tries to explain, but Blair screams at him, and says the whole night didn't happen, and then he's all alone. The end.
A week later, Jenny's at the train station, saying goodbye. Rufus hugs her goodbye, and Eric promises he'll always be there for her, in the city. Rufus gathers up his son and daughter in his arms, and then pulls in Eric and Lily. I'm guessing Serena is busy. Jenny takes off into the station so she can stare out the window -- like Serena, like Marissa Cooper once upon a time -- as the train pulls away.