Coming out of the Fifth Umbral Era – The Age of Endless Frost – magick was rediscovered as a means of survival, giving rise to cultures that highly valued aetherial arts. Cities rose around it, prospering in friendly rivalry.
Within this age, Shatotto developed Black Magick by learning to use environmental aether for spells instead of just the aether within ones own body. The potential for destruction seemed limitless, and the city of Amdapor created White Magic to act as a check and balance. With the info we have now, we think that the Black Mages were established the the city of Mhach, eventually moving from Black Magic into Void Magic. The third city we know of was Nym, home to the Royal Marines (Scholars and Marauders).
These cities, and possibly others, eventually had their friendly rivalry sour. The resulting realm-wide war, the War of the Magi, consumed them. Alliances were made and broken between various cities, but eventually it seems that Mhach gained the upper hand, summoning Diabolos to destroy Amdapor and unleashing the Nymian Plague that turned its inhabitants to Tonberries.
This widespread use of magick – environmentally fueled magick – upset the aetherial balance of Eorzea and ushered in the Sixth Umbral Era, a devastating flood. That’s about all we know – we don’t even really know how it all turned out. What little I’ve been able to puzzle out on my own suggests that the Archons (possibly the Sharlayans) raised an army of golems (which blade can’t scratch nor magick corrupt) and put down those who refused to cease hostilities.