Geological / environmental event
As if by a supernatural force, the first day of the thousandth year brought with it a mysterious cold. A cold that never seemed to leave.
It had been noticed ever so slightly throughout the year by the various species, however none of them thought anything of it. The changing of temperatures and seasons was a completely normal thing that the inhabitants of the world had come to know and understand - however none of them could have predicted the destruction this slight frost would bring in the coming millennia.