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First I would like to say that my knowledge of 40k fluff is not at deep as I would like, so i picked up a copy of "Horus Rising." I really enjoyed the read and can not wait to catch up on the series. With that I started to wonder about the Emperor's ideology for reaching ultimate unification with the lost planets of mankind. Now I realize that this may be addressed later on in the series or another book, if so I would love to know so I can read it.

What I got from the book was that the conquered planets pretty much had to throw out their old society and embrace the ways of the Emperor and of Terra. It hints at this in the book but what I don't get is why they would not be allowed to keep their old ways, unless it caused harm or major differences(Such as Aliens playing a large role in society or such) just as long they submit to Terra and the Emperor They could even share their technology (if more advanced) and serve as a sort of auxiliary part of the army. One would think this would make the worlds much more willing to embrace the Emperor, and easier to maintain, then they could slowly start to reshape the planets as they saw fit.

i suppose I can see the lack of a common culture being a cause for unrest though, and causing problems with the Space Marines with the introduction of auxiliary components in armies. It just makes me wonder what the Emperor's ideals really were when using such force and harsh doctrines for unifying mankind.

They don't all have to throw out all the old ways - only when they are in direct contention to a decree made by the Emperor.

The Interex, for example, would probably be able to continue just as they are APART from the fact that they consorted with Xenos - which is a crime. Their choice is to join the Imperium, and treat the xenos as the emperor decrees (KILL THEM ALLLLL!), or be considered an enemy.

They would get to keep their various other customs, as the Imperium trusts that continued interaction would make them more Imperial over time - that's also what the Iterators are for - to espouse the benefits of Imperial culture.

Tech is a similar story - often the Mechanicus would love to get their hands on the tech and peacefully share, unless it's counter to a holy decree - such as the artificial intelligences fought by the Word Bearers in The First Heretic.

I think the Emperor knew he had to hammer mankind into compliance, The 30th milleniums galaxy was a pretty rough place for humanity with individual human planets and empires falling easy prey to the predations of xenos races, plus I believe he was trying to weaken Chaos by starving daemons of worship by promoting the Imperial Truth. The Emperor is trying to achieve complete security of the human race by ensuring control of the Galaxy, you dont achieve this by playing nice, your either with Humanity or against it.

It also depends who's incharge of the occupation. Some chapters were more forgiving than others when it comes to integrating cultures, while others are alot more thorough or harsh in converting a planet.

Basically, he just had some hard rules that must be obeyed.
Do not consort with Xenos.
Destroy mutants.
Turn over all psykers.
No religon.
Pay your taxes (tithe).