The Caliphate of Man:
The Prophet (Emperor) appears to unify humanity, gifting a sociopolitical system/religion to follow calling for the conquest of the galaxy and technology, including transhuman augmentation to do so. Most importantly among this, FTL. It requires faith. Anyone but a genuinely faithful Navigator using the same equipment ends up daemon-chow, or worse, has to make a deal with them. Having unified humanity, He departs, offering to return when the unification is complete. The civil war (less Horus Heresy more Sunni/Shia split in that both sides claim loyalty to the Prophet's goals) begins in a matter of decades.
Fundamentally, it's a succession crisis over who'll lead the Caliphate, with a side of transhumanist kookery from the Mechanicus.
The Administratum claims hereditary rule. They're the descendants of the functionaries the Prophet himself put in place, therefore their lines rightfully belong there.
The Mechanicus on the other hand, want to specially design leaders. Perfected transhumans whose brains are wired to make them incapable of sin or doubt. Less servitors, more
peter watts abominations, with a long-term goal being that the
proper conquest of the galaxy necessitates discarding humanity in favor of computronium matrioshka brains to convert all matter into faithful minds and the support infrastructure of same. They can't actually do any of this, but they hope to learn how eventually, so for the moment it's just ideology and they want their magos, who're
completely coincidentally, the ones pushing all this ideology, to be in charge.
They may also be influenced some kind of necrontyr cargo cultism, some of their higher-ups found tomb worlds just before the civil war begun.
The split was resolved-ish by Caliph Guilliman who's both placed in his role by the Prophet himself and an transhuman designed for his role by the Prophet and more importantly, has survived every single assassination attempt.
Chaos:
Chaos tends toward daemonic deals. Offer x percentage of a ship's crew in sacrifice or worship them and they'll let it make one FTL jump undevoured, or give you useful mutations and the like. They heretically claim the Prophet is just the same as them, except this is mostly disproved by the Prophet's religion seemingly valuing the lives of the faithful for their own sake, while they don't. Less outright armies, more cunning corruption of whole civilizations.
Xenos:
Orks are rampaging berserkers essentially like canon, except they don't have FTL and that their backstory is more along the lines of their original appearance in canon than the modern bioweapons-made-by-the-Old-Ones-for-the-War-In-Heaven stuff. Caliphate xenoarcheologists have found proto-orkoid ruins, showcasing
a very different species, their current form was apparently deliberately genetically engineered to let them colonize the galaxy more effectively as space hulks of frozen spores which grow into creatures instinctively programmed with a viable techbase.
The Necrontyr were likewise without faith and its benefits. Millennia ago, they colonized the galaxy, but only at STL and as machines. Minds uploaded into robotic shells and egocast between worlds for travel. This turned out to be what spelled their doom, as they found virtual worlds superior to reality. Their tombs are server farms, hosting the uploaded personalities of entire populations in utopian simulations of their own making, with mechanical bodies ready for teleoperation if they ever lose interest. Until the self-repairing equipment wears out and they die. The only active necrons are those whose obsessions outweigh their hedonism and make them remain in reality. An anthropologist who wants to study the galaxy's new civilizations (Trazyn's gotta have pulled a Sir Richard Francis Burton at some point and infiltrated earth itself on Hajj, disguised as a human techpriest. And by 'disguised', I mean, in a very rudimentary fashion like a red robe over a clearly xenos mechanical body.
Hey, it worked for him in canon accidentally.). A soldier still defending the ancient boundaries of the Necrontyr civilization against trespassers.
A mad scientist going full mengele on captive marines and navigators to try and figure out a scientific explanation for how their bodies let them break physics so he can replicate it.
A hero trying to save his race by snapping them out of their dreamworlds, tomb by tomb, despite their total lack of gratitude.
The Eldar are a factory farm by way of the commonwealth/technocore relationship in Dan Simmons' Hyperion. The chaos gods have given them an interstellar portal network. Not that they'd believe in gods. Surely the occasional portal failures, very rare but they add up across an interstellar civilization, during which victims just disappear are coincidences, not
sacrificial offerings. And if anyone who finds out tries to use a
farcaster webway portal, they'll join them. A few Eldar know the truth and have either graduated to outright cultism,
offering extra sacrifices and worship for power in their society, or
fleeing to live outside the empire, without the secretly entrapped technology.
Tyranids are identical to canon, save for lacking FTL, hiveships can just dehydrate themselves like tardigrades and hibernate away the time between the stars. Best to get them when they're only a few light-minutes out, before they all wake up. Genestealers are a new and extremely unwelcome development, the hivemind learned about faith-fueled FTL and while it can't do it itself, it can make human hybrids which can hitchhike, then give birth to true tyranid organisms far ahead of the hivefleets without warning.
The Tau empire triumphantly plot galactic conquest with their fleets of bussard ramships and have already seized
dozens of nearby worlds, including subjugating the bronze-age Kroot. Now one of their colony fleets decelerates towards a human world with absolutely no idea of faith and magic and how hilariously outmatched they are.
Thoughts?