Spoilers for the story of Alexander released in 3.01 ahead.

So before floor 3, we're looking for a spy. Then it's revealed that the spy might be Brayflox. So we go inside and at the end the spy dies. But no one identifies the spy or says whether or not it's Brayflox or not. The quest journal says "You can only conclude that she is not who she seems." and the quest text just has Cid say something similar, but by the end of the floor there is no clarification.

Did I miss something? Or am I not noticing something that was shown? I'm still confused about the spy and where Brayflox is while all of this is happening.