The story is set in the years following June 29475; the current game year is 29482. The story of Anarchy Online revolves primarily around two factions, the hypercorporation Omni-Tek and the rebel worker caste, the Clans. These two factions are fighting for control of Rubi-Ka. In addition to these two, there is a third faction of Neutral observers, people who have decided to take no side in that particular conflict. The war has been waged on and off for centuries. In addition, there have been larger conflicts between Omni-Tek and other corporations over the control of Rubi-Ka.
Rubi-Ka, a seemingly useless desert planet, is of such tremendous importance because it is the only known source in the universe of the fictional substance notum. Omni-Tek, having been granted exclusive ownership rights to the planet, controlled notum for many years and benefited tremendously when it was discovered that the mineral would revolutionize, and eventually become the key component of, nanotechnology. The discovery of notum's properties led to the development of technologies that seem very much like magic, including programs that create things such as fire and ice, heal injury, shield people from harm, affect their physical bodies, and even achieve resurrection. Notum even makes its way into the very genetic makeup of some sub-breeds of humans.
Due to Omni-Tek's unfettered control of Rubi-Ka, the corporation was largely free to do as it wished with its colonists and the planet. For most of the early years, Omni-Tek did its best to treat its people well, even to the point of receiving commendations for its treatment of workers. However, over the centuries, Omni-Tek's policies degraded, until finally, approximately 500 years after the planet was first settled, a significant number of poorly-treated colonists rebelled and began to secretly trade stolen notum to a rival corporation. This led to a series of wars between Omni-Tek and the colonists, and between Omni-Tek and its rival corporations.
The background of the game is described in greater detail in the book Prophet Without Honor: Anarchy Online Book 1, by the Anarchy Online creator Ragnar T?rnquist. A detailed timeline of events, from the discovery of Rubi-Ka until 29479, is available at the official Rubi-Ka Timeline page.