The Lady of the Night story arc -MIGHT- get expanded on during the next update (due out next summer?).
As far as in-game knowledge goes, one can make a reasonably solid guess that Syllara, aka the Lady of the Night, is the cause of the people going missing. It's a pretty solid guess, but it's not explicitly stated in-game.
Based on the tons of other tidbits in the game, one can make a reasonable guess that the Lady of the Night story arc sets up for a Varannari vs. The Church of the Three.
Based on same tidbits as above, one could also guess the Lady of the Night arc would explain the origin of the three, and likely involve a fight between the main character and a powerful god-like deity, either Arbenos, Syllara or an yet-to-be named evil entity.
Quest decisions might determine how the main character fits into that showdown.
Keep in mind that the in-game tidbits show that Syllara only embraced dark forces as a means to fight for freedom of her people. It doesn't explain how, or who, helped her in that process. That opens the door for Syllara being painted more as a flawed, anti-hero than a truly evil person. But that would depend on how far she's gone into the dark.
Keep in mind that David the Developer hasn't released plot outlines so a lot is. at best, a educated guess.
