For example let's start with a simple question; why was our party tadpoled? On the surface that seems like a simple question with a simple answer that barely needs going into. But then you learn more about the events leading up to your escape and you realize that it doesn't make any sense why any of the party were abducted.
And how is it that the handful of co-abductees are nearly all closely associated/involved with some powerful entity? We can also add Gale's bomb thing and the fact that Karlach managed to sneak onboard. (But if she sneaked onboard then does she have a tadpole?).
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Having finished the creche/monastery I went to camp for a long rest then off to the Mtn Pass (did the Underdark last time). I entered the transition and found myself back at camp. No instructions as to why or what to do. I couldn't leave so I had another long rest which was broken by Voss turning up (never saw him last time). The Dream Visitor said not to trust him which completely threw me as I thought they were on the same side.
The Voss dialogue left me none the wiser. He knew there was someone inside the artefact but not who. So as far as I can make out there are two agents working against Vlaakith - Voss and Dream Visitor. A bit of a coincidence if that is correct.
More a bug than anything but I have had a journal entry telling me I missed Dammon in the SC lands or the inn but hopefully I can still find him in BG. The entry has been there since long before I steeped into the SC lands and now I have just arrived at the inn there is Dammon working away in his little corner.