The Argons are commanded by , the Argon Queen. The exact reason behind the Argons invasion is unknown, but it's clear they aim to eliminate all life and change the world of Arborea into something else.
The Argon War resulted in the creation of the Valkyon Federation, a coalition between all seven playable races in TERA. The Federation aims to defend all of Arborea and fight back against any who would harm the world.
The so called First Argon War and heroic deeds of defenders of Kaiator actually took place while player character was noob patrolling Arcadia. Chronicles of the Argon War tells how war congress was organized in Velika, where it was decided to raise large and well-equipped army to counter this alien thread. This eventually led to creation of Valkyon Federation. It was Elleon and Syona who created flight path to Susurrus Woods where troops from Allemantheia gathered and marched to Kaiator.
Story from player viewpoint only happens after the First Argon War and after so called Cold War, after Argons were defeated in Kaiator, and after they suddenly retreated from Thrallhold, leaving behind argonized territory and monsters.