The conflict was led by the Gods who hated their masters, but were forbidden from raising their hands to them by a powerful geas. Therefore, aided by the renegade Autochthon, they placed shards of their Essence into mortal humans and created the Exalted to fight on their behalf. The humans, also hating their subjugation under the Primordials, readily agreed to fight.
The war ended with the utter defeat of Primordials, the Gods ruling Yu-Shan, and the Exalted in control of Creation.
In the early history of Exalted, the Primordials ruled Creation from the celestial city of Yu-Shan and stayed in Heaven to play the Games of Divinity. The Gods were in turn delegated to the maintenance of Creation, administering reality from the Blessed Isle. In this era, the Celestial Incarna grew envious of their creators and desired to have the Games of Divinity for themselves. The also felt burdened by servitude that felt like slavery to them. However, the Primordials had bound the Gods by powerful oaths during their creation, and the Gods could not attack or otherwise harm their makers directly.
Some incalculable time after the beginning of creation, the Unconquered Sun devised a plan for revolt. He made secret alliances with the Primordials Autochthon (always mistreated by the other Primordials), and Gaia (who had by this time abandoned Cytherea for a new lover, the God Luna), as well as selected Gods throughout creation. To the Gods he selected, the Unconquered Sun high offered positions within the coming new order, and the ownership, rather than the mere stewardship, of reality.
Many other intelligent races lived in Creation besides humanity and spirits, and most of these sided with the Primordials who they revered or worshipped. A few, such as the Genesis Lords and Pelagials, attempted to survive the war by remaining neutral. Only the Dragon Kings who worshipped the Unconquered Sun, and the Jadeborn children of Autochthon, chose to side with the humans and Gods.
The exact details of the Primordial War are unknown. What is known is that the foremost weapon of the Gods were the Exalted, humans gifted with divine power through a process given by Autochthon to the Unconquered Sun. These Celestial Exalted and Terrestrial Exalted were armed by Autochthon and the Jadeborn, with powerful magical weapons that the Primordial had designed. The leadership of the war was under the control of the Unconquered Sun, but the tactics that won it were developed by the Maiden of Battles. The Yozis themselves fought alongside their many loyal creations, using the same reality-bending and time-twisting powers with which they had built Creation at the dawn of time.
The war reached a crescendo with slaying of several Primordials, a feat previously believed to be impossible. The slain became the Neverborn, and their deaths created the Underworld and the first Shadowlands. The remaining Primordials fled or surrendered, and those surrendering were exiled and imprisoned in a Hell created from their own bodies and the exile of the others, becoming the Yozis. The dying curses of the Neverborn created the Great Curse, although its full impact would not be felt until the end of the First Age.
Humanity and the Gods achieved their freedom from oppression and slavery, but at great cost. At the end of the war, with the vast majority of the Primordials either dead or subjugated. Only four escape unharmed: Gaia, Autochthon, and two others who fled into the Wyld rather than surrender. Of the two remaining, Ramethus returned to attack Creation during the First Age was slain during the Aftershock War. The other has never been heard from again.
The Exalted were promoted to rulers, guardians, and stewards of Creation, taking this role over from the Gods. The Gods, in turn, retired to Yu-Shan. The highest Gods took play at the Games of Divinity, while the rest took new roles in the Celestial Bureaucracy, ultimately under the rule of the Unconquered Sun.
The prehuman races who worshipped the Primordials, including the Lintha, Alaun, and Uddshua, were driven to the brink of extinction or beyond by the genocidal victors. The Genesis escaped genocide only by fleeing into the Wyld, despite their neutrality. The surviving older races, the Mountain Folk (Jadeborn), Dragon Kings, and Pelagials, slowly fell into obscurity through senescence or mystic oaths imposed by the Exalted. The newly formed Underworld became a sinkhole of Oblivion, damaging the cycle of reincarnation and ultimately making the Great Contagion possible. Gaia and Autochthon fled Creation at the first inklings of the Curse. The world entered the First Age of Man, and the seeds for the Usurpation were already sown.