“This is a really sweet moment because she’s accepting him back, but he’s saying “Look, if you really don’t want me here…” and it’s a nice little dance that they do. This is where they’re saying they like each other without saying they like each other. One of the reasons we wanted that line for Beckett “See you tomorrow” is that in the end of season two, in that episode, the last thing she says is “See you in the fall”, and it’s more with a question mark, and Castle says “See you in the fall”, but it really is unresolved, and now that things are back, things are normal, we’ve reestablished the relationship. “
(Andrew Marlowe, Rob Bowman, and Nathan Fillion episode commentary)