User blog comment:Wiz Ardon, the Peculiar Enchanter/The Story of a Minifigure: Strange Odd Shadow Rewrite Chapter 4/@comment-27324808-20170705141908/@comment-28549248-20170705150647

The following might get a bit spoiler-y (concerning what the unknown enemies are), but nothing you wouldn't really expect, I think. Wait, does that reveal the truth on its own? Dang it.

If you look at the missions in the wiki, I believe you'll find that the term "Spider Queen" is first mentioned by Vance Bulwark, as it is indeed originally a mystery as to what's causing the clouds. As for the number of Spider Queens, I try to stay as close to the original LU plot, but within reasonable realism. It seems more logical that there were many Spider Queens spread over many Block Yards so that different recruits faced different Spider Queens to claim different properties. That's also why you can face the Queen again. Because there are many of them. Note, though, that a Spider Queen is not a Spider Boss. That's unique and more powerful.