I think the only way to do this would be to draw inspiration from all the popular world ending story hooks. I.e Armogeddens, death plagues, illuminat puppeting everyonei, Aliens invading, Nuclear war and so forth.>Faction transplants.
Salvation war's hell (X4) for each chaos god would make a good chaos faction.
Skaven from warhammer can pretty much just be transplanted in as they are now only with their everything being more plentiful and better.
Elves can be a lost city of Atlantis type deal with ancient temple cities hidden under the ocean where the elves act like the iluminati and generally be dicks about it, lots of psyonics running around on surface missions to control stuff and hoards of superweapons.
Orkz are niggers xdxdxd:D get it? Because Orkz are violent and blacks are also violent. They can like, overrun a bunch of 3rd world shitholes.>Original factions
A chaos gods mirror of order/blatent heaven expy and use them to weave up a clear dynamic of the two trying their best to take as many mortal souls as they can get their hands on to empower themselves aggainst the other.
A blatent expy of the Migou from cthulhutech to serve as the alien invasion role and tyranids expy.
The humans revert back to Cold War relations that are more akin to 1984 then the actual Cold War.