The Elementals were created by Ancient Dragon Witches by exploiting the reality altering powers of the Genesis Molecule. The Elementals were created to be the Dragons' avatars to interact with hostile and distant worlds either inaccessible or too risky to approach physically. With the tendency of in-fighting amongst the overjealous Dragon Witches, advanced Elemental creation became a political competition that got out of hand. In short, they gained free will and rebelled.
Elemental Seperatists joined the Great War solely because without the Molecules, they would have been extinct. After the war, Elementals, like any other faction, suffered severe damage. While most of them were annihilated, the rest fled back to Twisted Clouds to carry out an uneasy truce with Beasts and Dragons.
"Elementals don't have memories... memories fade. What they have are permanent, collective and decentralized records of facts. History never escapes them... never cross them the wrong way!"