Old One
Arcane
Since I just completed the game I will say I got the impression from the writings in Hellgate and the Ziggurat that the Magi survived the war and might have been able to rebuild the Empire to a certain extent if Agathoth's Magi followers hadn't refused the order to banish his essence back to the void. The war seems to have been a continuation of some pre-existing conflict between the aliens, with Baalzor's faction on one side and Agathoth's on another. Baalzor used the Qantari as his tools, and Agathoth used the Empire. Agathoth won the war and was the sole alien remaining on the human side of the gate, but the leadership of the Magi no longer trusted him and wanted to banish him anyway. The refusal of Agathoth's minions to comply with this order started a civil war that destroyed the last of the Magi and the last remnants of the Empire. Agathoth only survived because his disciples sacrificed everything to make sure his vessel wasn't destroyed.