My ideas for the thing that wrecks everything
1.Extra-Universal threat, possibly Reapers or Borg
2.Insanity escapes and being the God of Chaos wrecks everything

Also yes technically we are still smashing everything up and just shoving everyone back on there homeworlds but there are remnants of the old civs so its still a sequel rather then a total reset. The technology would take a bloody long time to decode though.

Also as to why Faust wouldn't intervene is because she prefers subtlety and slight pushes to get people going in the right direction, she doesn't usually do direct intervention.