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 Dwarvish citizens, but also created the Skaven- the end result of both regular rats and the 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, which was 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 center of the city that housed the first Screaming Bell. From the church, those Skaven that had survived watched as twelve grey-furred rodents stepped out, speaking that they were the ones who had been chosen by the Horned Rat to lead their people, as ordained by the Horned Rat.
Since then, the Horned Rat has served as the symbolic leader of the Council of Thirteen - the Skaven's twelve most powerful leaders, with the 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 in the Skaven's lives than realized- just not as expected. Rather, he serves on a second council- the Shadow Council of Thirteen, forged of himself and the Verminlords- rat demons and deities alike for the Skaven -of the twelve main clans of the Skaven.
For the most part, the Horned Rat stays in the shadows, watching his children quarrel with one another, sabotage other races and cause general mayhem in the world. However, on rare occasions, the 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 his presence will be more keenly felt.
Recently, the Horned Rat has been able to ascend into the pantheon of the Chaos Gods; though regarded as lesser by his peers, it's only a matter of time until he becomes as dangerous as the other dark gods.