Anarchy Online stands out for being one of the few popular MMORPGs which is not based in a fantasy setting. Instead it is set almost 30,000 years into the future on the planet of Rubi-Ka. Instead of the use of magic, unusual skills the player may acquire are explained through the use of nanotechnology.
The background to the story played out in the game is that the large 'Omni-Tek' corporation received the exclusive rights to mine the planet's valuable natural resource of 'notum' which is vital for the development of nanotechnology.
Shortly after arriving on the planet, a significant number of the colonists opted to rebel against the Omni-Tek corportation following poor treatment and conditions, and began to secretly trade stolen notum to a rival corporation. Eventually they started to drive out Omni-Tek people from the outlying cities and there began a civil war which rages to this day between Omni-Tek, the Clans, and a third faction, the Neutrals, who ally themselves with neither side, but instead seek to lead peaceful lives.
The background is described in greater detail in the book Prophet Without Honor: Anarchy Online Book 1, by Norwegian author Ragnar Tørnquist.
A brief online summary of the history of Rubi-Ka is also available at the official Rubi-Ka Timeline page.