Writer! Anon here: There are a LOT of secrets between the two that they're not aware of. So no, Thomas doesn’t realize that Connor was the native girl they stumbled across all those years ago. And Connor was so focused on Lee that she can't quite remember that he was there either. Not to mention, Thomas doesn't realize she's Haytham’s daughter, which is bound to put them in some pretty difficult positions in the future. Needless to say, these two have a ton of hurdles to get through before they can have an emotional relationship on equal footing without deception and angst. And that's assuming they even can make it that far. Of course, from the prologue, it definately gets physical pretty early on.

...and yeah, this is turning out to be a lot longer than I ever thought possible. It's turning into full blown AU territory now!