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From Warhammer 40k - Lexicanum
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Even while the Imperium was collapsing under the weight of rebellion, further dangers befell humanity. In early M36, warp storm instances increased and warp travel became impossible between most planets. With the resources of the Administratum and Ecclesiarchy centred on the power struggle, massive areas fell to anarchy as they became cut off. Those planets which could still be accessed by starship were patrolled and controlled by the Ecclesiarchy with an iron fist. Burnings and executions became commonplace of all but the most faithful.
[[Chaos]] raiders poured from the [[Eye of Terror]], Ork [[Warboss|Warlords]] rampaged across the galaxy and nobody could halt them. On the isolated worlds, Chaos and [[Genestealer Cult]]s grew up, overthrowing the governments. Those worlds not overrun struggled to survive and eventually even the greatest of the planets collapsed. Even worship of the Emperor collapsed without direct leadership, most people splitting into cults that worshipped the Emperor in their own way and tried to force their ideas on the other cults forcefully.
Crazed zealots across the galaxy denounced the Ecclesiarchy and preached that the Emperor was displeased with their greed and excesses, sending the warp storms as a test of the most faithful. Citizens turned to flagellation and self-mutilation to prove their love of the Emperor. The cults grew and fought and settled into seething masses of discontent, while some preached extreme measures, creating bloodthirsty pogroms to eradicate many innocents. Sometimes, whole populations were slaughtered for the heresy of just one person.