Part I: The Brotherhood
For all purposes, the Brotherhood ceased to exist on the day of the invasion.
On that day most senior members were out of town. Captain Thenthen led the resistance in the markets, and those of the Ra clergy who were also members of the Brotherhood presumably died defending their temple.
Accordingly there should have been little enough resistance in the Brotherhood tower – certainly nothing to explain the sounds of fighting and screams that went on in the tower for many hours. After the fighting had finally left off, some people swear they saw a giant shadow fly from the top of the tower, but that is something that has probably to be ascribed to the fantasies of those poor souls.
It is clear however that the imperial investigators who entered the tower the following day found nothing besides dead soldiers, and all things of value seemed to have been taken away.
Captain Thenthen and Lady Liamyn continued to lead the fight against the Empire from Vesper. About the fate of archmage and former captain Deldor Colds nothing is known. It is possible that he died during the invasion or that he managed to escape, but he hasn’t been seen since that day.
Even though most senior members survived the invasion, most of them turned to other duties in order to fight the invaders. The tower served as a headquarters for the imperial army for some time, until it was reduced to a heap of rubble by the combined efforts of Lady Mage Liamyn, High Mage Shessair and Archwitch Naredia during a raid a few years later.