The Horned Rat's origins can be traced back to the World Before Time, with the creation of his people thanks to the toiling of an unnamed mortal clad in grey. His work -- the creation of a Screaming Bell -- brought an entire city low and destroyed not only its Human and Dwarfish citizens, but also created the Skaven -- the end product of both mundane rats and the Human children of the city being exposed to the mutating effects of Warpstone.
With the fall of the mortals, the Skaven proceeded unopposed to overtake the city's subterranean ruins, which were dubbed Skavenblight. The Skaven first became aware of the Horned Rat's existence following a failed attempt to expand their already substantial home -- some unforeseen wrench in the works of a great tunneling machine destroyed every building in Skavenblight, save for one -- the large church in the centre of the city's ruins that housed the first Screaming Bell.
From the church, those Skaven that had survived watched as twelve grey-furred rodents stepped out, who proceeded to explain that were the ones who had been chosen by the Horned Rat to lead their people, as ordained by their scabrous new deity.
Since then, the great Horned Rat has served as the symbolic leader of the Council of Thirteen -- the Skaven's twelve most powerful leaders, with the Great Horned Rat claiming seat 13, the most powerful spot on the council.
Unbeknownst to the Skaven, the Horned Rat has much more of an active role its children's lives than they realised -- just not as expected. The Great Horned Rat serves on a second council -- the Shadow Council of Thirteen, forged of itself and the Verminlords -- rat daemons and deities alike for the Skaven -- of the twelve main clans of the Skaven.
For the most part, the Great Horned Rat stays in the shadows, watching its children quarrel with one another, sabotage other species and cause general mayhem in the Mortal Realms. However, on rare occasions, the Great Horned Rat will deem it necessary to personally interfere in the affairs of mortals.
This has usually occurred whenever a Skaven civil war has gotten out of hand; this has only occurred twice, but the restoration of the Skaven as a species could mean its presence will be more keenly felt.
Recently, the Great Horned Rat has been able to ascend into the pantheon of the Chaos Gods; though regarded as a lesser deity by his peers, it's only a matter of time until it becomes as dangerous as the other Dark Gods.