The First Rune War (2751 BLE–2600 BLE) ended the Age of Divinity and marked the establishment of two great alliances, the Magelords and the Protectorate.
The War Begins
The First Rune War began in 2751 BLE. It was fought between two newly formed alliances: the Magelords, who controlled southern Valoran, and the Protectorate, which controlled the north.  Only Shurima stood apart, relying on defensive elemental enchantments to wall itself off from the carnage.
Temporary Peace and Return to War
The gods ended the war by force, channeling their divine power to reinforce Valoran's leylines and thus preventing rune magic from cutting into these massive thaumic energy flows to power rune spells. This led to a temporary truce, which ended in 2695 BLE, when Protectorate Summoners invoked the Rune of Freedom to break the divine seal and unleash rune magic on a Magelord stronghold.  The gods had bound their essence with the leyline-seals that the Rune of Freedom destroyed, and the breaking of the seals effectively ended the Age of Divinity, with most gods and elementals being banished from the mortal plane or corrupted into monstrous beings that took refuge in the deep ocean.
Resolution of the Conflict
The First Rune War ended circa 2600 BLE. The Rune of Freedom had filled Valoran with monsters and demons, many being the twisted remnants of the gods and elementals that ruled the Age of Divinity, and the Magelords and the Protectorate agreed to combine forces against this shared inhuman threat.
Together, the Magelords and the Protectorate forged the Rune of Purity, which warped Valoran's arcanosphere to become toxic to supernatural beings. It also disrupted Shurima's elemental magic, and ruined that once-great empire in a cataclysmic event known as "the Scorching of Shurima".
The Rune of Purity had a further effect, subtler at first: it impressed upon mortal beings a psychic drive toward ideological purity, such that they began to revere their nation-states much as they had once revered their patron gods.
Valoran remained more or less at peace for about 200 years, until the Second Rune War began circa 2400 BLE.