I've just regained Imoen, and attempted to leave the island by ship. Having completed the Sahuagin quest, I've (for no apparent reason, beyond it being the only way the game would let me progress) descended to the underdark, and now my character seems to know that Irenicus and Bodhi are down there too. Did I miss some dialogue where I was told that was the case, or something? I'm currently very bewildered.

Should I pretend that the royal high priestess told me that Irenicus and Bodhi were down there? The entire quest seemed to be somewhat bugged, with most of the sahuagin on both sides being marked as enemies and attacking me from the start, other than the guards/priestesses, and the royal high priestess and the guard commander died when I agreed to help the rebels.

There are several clues, and the Duergar trader you meet right at the start of the Underdark tells you so: he talks about "the neck biter and the mage".

It was that very conversation that I was confused about. By the route that I'd taken, at that point the only 'clue' (which I'd seen, anyway) was Saemon saying that the portal could lead anywhere, 'even to the underdark'. I had the option to ask about two other surface dwellers who would have passed through recently before he mentioned them.

It's a condensed clue trail. You are not going to get expansive reasons in a game like BG. The clues are there, if you follow the dreams, cut scenes and conversations with other npcs.

Ok, I'd been ignoring the cutscenes from the point of view of in character actions, as, so far as I can tell, my characters are unaware of them (obviously with the exception of the earlier ones, which Imoen will obviously have seen and shared with the rest of the group). Out of character, I realised that they were in the Underdark, but in character I didn't. If that makes sense. Mind you, in character I have an intelligence of 8 and a wisdom of 21, so maybe I intuitively guessed it :P