The strongest theory I've heard is that it's a metaphor for Randall's wife's cancer (ie "the sea" == "the C"). Lines like "the sea can't keep making more of itself forever!" and "we don't understand how the sea works" lends a bit of credence to that.

I suspect that Randall would prefer that at least one of his comics wasn't interpreted as a reference to cancer. It must get tiring after a point.

I'm not aware of any other comics being interpreted as a reference to cancer, but there are a handful of comics directly referencing his wife's cancer. If it is a recurring theme of his, I'd say it's perfectly legitimate for people to consider it a candidate for an otherwise unexplained plot line.

The discussion on the xkcd forums frequently attributed every single comic to be a cancer reference. The forums have since been removed from the main page though. so it's not quite as visible anymore.

Yeah, that's what I got from it pretty quickly.

The castle is the carefully-constructed life they've built together which is being encroached upon, and they abandon their previous endeavor to find the cause or whatever.

And, naturally, the journey becomes the focus rather than the end goal.

The plot is (only a little) simplified, but this seems like Randall's 'novel'.

What lack of a goal? They are trying to figure out why the sea level is rising. (Possibly because they think the rising sea will eventually destroy their castle.)

I'm not sure it is much to do with the castle. There's a vague mention of tents getting wet and other people noticing.

All a bit odd really, and the dialog really does say "on drugs" to me...