Rachel was alive through LIS.
I've seen this theory here and there in comments, but cannot find it anywhere else.
So the theory goes that Rachel was actually alive up until around the last time we see Nathan. In the dark room, we see the photo of Rachel in the junkyard, presumably dead. Nathan's body is under hers. Why is that? I mean I know the kid had some issues, but it really seemed throughout the game that he was troubled by something or someone (Jefferson). I don't think someone would go from posing under a dead body of a friend to resenting an accomplice so quickly. An accomplice who, if Nathan had posed under Rachel's dead body willingly for a photo, had a load of shit on him.
So I think that Rachel was alive. She was quite rebellious and didn't seem to care if she hurt people- so what if she had just done what Jefferson said because she as we were told had a relationship of sorts with him? She wanted to be a model and Jefferson was a great photographer who had connections. So what if she wasn't missing, but had willingly shacked up with him? Or maybe she really did make it out of Arcadia bay but came back to see Jefferson, who again, she was supposedly obsessed with. If not, perhaps he made her.
Now, that let's put that aside. Jefferson mentions that Nathan lusted over Rachel and we all know that Rachel held affections for others. I think that Rachel was alive, whether she was hiding or kept, and something happened that caused Jefferson to snap. Maybe Rachel wasn't ok with what he did to Kate and tried to leave. Wouldn't Nathan have helped if he lusted over her? Or maybe Jefferson didn't like his prodigy lusting over the Rachel. And so Jefferson kills them both around the last time we see Nathan. He gets them both to the junkyard and poses them for one last photo. Then he pins Rachel's murder on Nathan, who is dead and therefore cannot argue it.
Note, in the photo of the bodies we see Nathan wearing a dark cardigan, which we can see in other parts of the game under his jacket. In the dark room Nathan's jacket, which he seemingly always wears, is left on the sofa. Also Rachel's grave was shallow; surely if she was killed around the time of her disappearance, some wild animal would have dug that grave up over the months? JUST A THEORY.
Hope i explained this well enough, I think it's an interesting theory and works