Wah?

Behind on most of my shows, among other things, and I'm plodding forward.  Just saw the Castle episode "The Time of Our Lives."  WTF?  I mean, it was a cute episode and the ending was a) lovely and b) a long time in coming, good job finally getting it together, show.  But seriously, what was this plot?  I mean, I'm an SF buff, I can suspend my disbelief through a departure from the possible, but only if that has been telegraphed to me by the plot of the program in advance.

You cannot go 7 seasons having everything be essentially real-world logic with occaisional departures into silliness and a handful of plotlines which could be explained by supernatural means or natural ones depending on how you want to take it, and then be like "Oh hey, alternate universe episode kids.  Bye."

I just don't get it.