At first, the cities were ruled as a single entity by a sinod formed of the elders of the cities, ruling in God's name and overseen by the Angels; however, after the Nephilim appeared, anarchy and chaos overtook the cities, and more or less powerful warlords carved their own petty domains, using the Giants as weapons. When God sent his angels to clean up the mess, the common rabble was turned into the monstruosities that roam the ruins of the cites, and the most powerful and cruel of these warlords were sent into the Prisons for an eternity of torment (and that's you). 

(please note that by "warlord" I don't mean a necessarily warrior-type character: it can be also a dark magician, sorcerer, necromancer or whatever; it just needs to be "evil")