Originally Posted by
Mad Mask
Artificial intelligences.
Really. I'm not talking about the smart as dogs Tau ones, or the souls-in-machines Necrons, but autonomous solar-powered AIs who continue to improve battle technology and manufacture unmanned combat vehicles. The Imperium previously eliminated all "Abominable intelligences" during the Dark Age of Technology; what if one artificial intelligence, before the crusade, was lost in the depth of space in a freak warp accident ?
Left to itself, it continued to improve its weapons, building similar AIs and regarding every lifeform as an enemy. The new fully robotic faction finally encountered the Imperium again in the 41th millennia, and unsuccessfully hunted down by the Imperial Guard. Now seeing the Imperium as enemy, it is conquering planets after planets, heading (of course) for Terra itself.
EDIT: Although they are not really over-the-top enough...