Chaos and The Four Powers
This is the 'root of all evil,' or at least is portrayed as such, in many canonical sources. Generally created in a system of abstract, rigid and simplified 'alignment' seen in many fantasy games (i.e. 'chaotic', 'evil', 'neutral', 'good', and 'lawful') the Chaos Gods are capricious beings who - somehow - go beyond the Crowleyian concept of "Do what thou wilt shall be the whole of the law." They are created from the fabric of the Warp ('immaterium') by the negative, or 'evil' emotions, representing war-bloodshed (Khorne), change (! Tzeentch), plague-decay (! Nurgle) and pleasure-pain (! Slaanesh). Their goal is to merge the 'immaterial' (i.e. the Warp) with the material universe in the same way that the psychic backlash of the "Fall of the Eldar" created, or helped create, the Eye of Terror. In so doing, all of their 'evil' (or more precisely 'chaotic') followers who gain their favour are mutated over time into Lovecraftian horrors: tentacles, suckers, magical powers... the works.
I have a mental image of a follower of Tzeentch trying to work as the 'power behind the throne' to subvert a planetary governor, who is now quivering in terror before an Inquisitor:
"Who is to blame for this rebellion against Him On Earth?"
"My most trusted lieutenant is possessed by Chaos, m'lord..."
"What makes you say this?"
"Well, the fact that he's got a tentacle for an arm and the sigil of Tzeentch branded into his forehead, sire!"
"How have you acquired knowledge of Chaos little man? Die for your heresy..."
"Right, that's easily dealt with," says the Inquisitor, holstering his smoking laser pistol, "Quick, loyal troops of the Imperium: go and find people with mutations - those that not killed by the frequent purges by the once-loyal Governor, of course - and kill them. Oh, not the ones with three eyes of course since they're Navigators and on our side, but that goes without saying. Okay, time for a cup of tea..."
Well, okay, it's not exactly like that but the Cthulu-style 'inner deep' things are not my personal favourite and thus I've changed them slighty...
Changes here are mostly in terms of ultimate description and motivation of the 'LORDS OF CHAOS', though they are still fantastical. The Four Powers are altered to extra-dimensional beings that have been 'vastened' through superscience - probably a combination of computers and psionics technology - to beings of incredible power. While they draw their power from numerous proto-dimensions - 'Otherworlds' or the 'Realms of Chaos', i.e. that which lies beyond the upper manifold - it primarily derives from the upper manifold itself, or the 'psi plane'. Psykers draw the energy to power their abilities from this plane and, in essence, are 'hurting' or otherwise affecting the LORDS OF CHAOS. The 'demons' are psionic creatures without the 'magical powers' of the dæmons from c40k (though arguably psionics are just another representation of magic!). They are still considered 'evil' by the inhabitants of the material universe (primespace), but as stated in Mercedes Lackey's Magic Pawn (IIRC): "Evil done in the name of Good is still Evil, and Good done in the name of Evil is still Good."
How To Fix It:
Go back to the original concept, drawing more influence from Lovecraftian novels or the Call of Cthulu™ (Chaosium Games Inc.) roleplaying game. GURPS™ Special Ops and Cthulupunk would be useful, though scatter liberally with forced-modifications from the "Racial" section of Compendium I (use Secret -30 quite frequently), etc. Use Fright checks even more frequently and remember that any PC (other than an ordo malleus Inquisitor and Space Marine) will be executed for coming into contact or otherwise having knowledge of Chaos. If they find out about it, that is.
Technology in c40k is treated as an entirely narrative concept and, quite rightly so for a minitature-based wargame, around specific items or technology concepts. Machines are attributed with spirits, and technology of the Imperium is ultimately controlled by the Tech Priests of the Adeptus Mechanicus. Technology is a patched combination of tech-levels, with slugthrowers used next to blasters, powered combat armour and spatiotemporal distortion grenades. Other races seemingly only have 'relic' technology or 'weaker' technologies. While this creates a fantastically fun wargame, one which I heartily recommend, it does create a background which is in GURPS™ tech-level terms... inconsistent. Also, without a detailed knowledge of the background, what the various figures/armies can do, it is difficult to get a true 'flavour' of the setting. (Which, obviously, is also an argument that can be levelled at Rogue .)
A TL has been settled on for each of the races in Rogue. The Imperium is slightly strange as it is considered TL8-10+: TL10+ is controlled by the Adeptus Mechanicus, and lower TLs are available to all characters at cost (which varies depending on TL and social status - the rich and powerful always have better access to high TL!). This is interpreted as a further mechanism of control by the Imperium on trade and cultural diffusion beyond that brought about by the Navigators, i.e. the Warp drive (Hyperdrive-10) may only be manufactured and repaired by the Adeptus Mechanicus. The Eldar operate at TL12 (relic TL13-14 and 16!); Orcs at TL7-8 (relic TL9); Slann are TL3-4 (relic TL13-14+; psionics technology at TL-11); Tyrannids at TL10-11; Necrons at TL12 (relic TL-14); Jokaero, if introduced, are 'gadgeteers'; and Chaos at... anyone's guess, but ranging from TL8 to superscience.
An important distinction, however, is that access to technology does not necessarily indicate that the technology is used.
How To Fix It: In the Imperium simply put all technology under the control of the Adeptus Mechanicus. Commonly accessible technology will be TL8, with light military technology (handweapons, etc.) at TL 9. The majority of other technology will be unavailable accept by GM decision upon the accessibility of said technology to the player and/or organisation in question. Drop other TLs by 2 (1 in the case of Orks) and freely scatter relic technology from TL12-16 as per the background material for c40k.
Humanity is ascendant! is the essential motto of c40k which, given the background, is again entirely appropriate. All the other races - with the exception of Necrons and Tyrannids (and not counting Chaos since that is a special case) - are devolving, having fallen from their heights of technology and culture. Unlike the Imperium, however, their cause is lost and all that they can hope is to go silently into the night...
In Rogue the main changes have been further background material when it has not been available in c40k or, at least, that the author has access to. Information on the Imperium derives from a synthesis of Roman and medieval history. Eldar society draws from Perrin (1988) and a number of anthropological texts regarding clan-based chiefdoms. Necrons draw upon various 'cyberpunk' literature and films (Terminator, The Matrix, etc.). The other races I've no idea, but I've probably pilfered the ideas from somewhere.
Also, remember that as with any GM-created world, I've slanted things to my own perception. Not only that I've set it up so that the universe goes in a slightly different direction.
Change the direction! Generally ignore the background material that has been added to flesh out the races and their respective cultures. Ignore any included moral relativism (see above), which you should do anyway if it makes you uncomfortable, and stick with 'alignments' (see GURPS™ Mage the Ascension for ideas on how this might be included in terms of game mechanics, otherwise just apply reaction modifiers (c40k is generally cinematic and it is often possible to 'sense' an individuals alignment!))
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