According to a friend of mine she's supposed to be in a secret room behind the doomsday device (which is right next to where you fight Isibel) but for some reason she never spawned in my game.
When I ran into the secret room (which is accessed through an invisible wall to the left of the machine - taking the door to the left leads into a deathfog trap) I ran into some dead guards which caused my character to exclaim that the queen apparently could handle herself in combat.
Based on what my friend told me she's supposed to be in the room I ran into, but she never appeared in my game. I suspect the game's bugged and somehow made her despawn which honestly is a huge shame because I'm pretty sure I was at the final part of Beast's personal quest.