Mildly Darkened One
As far as I can tell, it's more like an environment becoming toxic than an infection. "Poisoned" supernaturals have their powers and weaknesses go haywire - but it also messes with God Machine Infrastructure, and presumably other supernatural places of power. The factions divide into Sworn and False - each has its own theory of why the Contagion happens - and their own idea on how to combat it (if Sworn) or use it (if False).CoD monsters infected with something that changes them and now it's all down the drain?
As stsword said, the Contagion is presented as something necessarily new - rather it's something that's occasionally happened throughout history.
I've asked, and been told the answer is yes, that the book provides advice on crossover chronicles without the Contagion as a framing factor (the same way as you can run Vampire with or without the Strix or Werewolf with or without the Idigam). Including, which I also specifically asked, making the Sworn factions robust enough that they could be used without the Contagion impelling their creation.