This is a repost of the link at the bottom of this post, I'm just moving it to a more appropriate category.
I seem to have an issue where Benweth went missing, but I didn't kill him.
Without progressing far into the quest, I went up to the command space, sneaked and triggered the bell to open the secret door. When I stepped it, the game triggered a conversation with the captain, which was supposed to end in combat, but since I was sneaking, the combat didn't trigger. He was