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I was thinking of an IG homebrew for some time now, and I know many people have different opinions when it comes to this, but so far it has just been more of a thought experiment than anything else, also I'm terrible at conveying details so bear with me and if your going to tear me a new one at least make it funny. any helpful input is welcomed, sarcastic and/or snide remarks also acceptable.

Premise: A Sector (terrible at naming things so, yeah) within the Segmentum Tempestus, in it lies (Name WIP) The Republic, The Republic is a semi autonomous interstellar nation (more on that later backstory time).

Said Backstory Bit: During the Great Crusade, Forces of the Iron Warriors were having significant amounts of difficulty attempting to subdue The Republic, as during the crusade they fought forces using similar equipment to the space marines forces, similar to the Auretian Technocracy. However with the arrival of Imperial reinforcements in the form of Imperial Fists, much to the displeasure of both legions, more progress was made, but for every two steps forward it was one step back, The Republic started to face internal strife and eventually negotiated a peace agreement, they were no longer able to use power armor and other such equipment that would be otherwise recognized on a space marine, they must recognize The Emperor as the absolute ruler of Mankind, they may never raise arms against The Imperium, The Republic would routinely be inspected by Imperial Representatives (Later Inquisitors), they must pay a tithe in resources and occasionally man-power to The Imperium, and would lose much of its territories to The Imperium, in turn The Republic will maintain it's independence, it will remain outside the Administratum and no space marines would recruit from their worlds.

About That Semi-Autonomous Part: After the Horus Heresy and into the 40k we all know and love, the peace agreement would be slightly revised during modern times, allowing for the Cult Imperialis and Cult Mechanicus to be practiced in The Republic, this would be allowed, although not enforced or mandated by the government (which almost led to a second war with the Imperium), the Cult Mechanicus however was more of a front for the actual technological society of The Republic so they could work from prying eyes, this leading to a rise in Tech-Priests commiting acts that would be deemed heretical, drawing in members of the Dark Mechanicum and other Hereteks. The border between both The Imperium and The Republic is patrolled regularly and nearly religiously by both sides. The Inquisition censored most information about The Republic, so to many other Imperials it is just another part of The Imperium.

Foreign Policy More like Foreign... Lame...: The Republic is a lot more lax in it's policies regarding aliens, The Imperium says they should all probably die, The Republic says they should all probably die if they f*ck with us. The Republic holds many Diplomatic and trade relations with both the enigmatic Eldar and the expansionist Tau, this has led to many issues as The Eldar are just at bad at explaining things as I am, and the Tau are like that one teenage guy or girl who's into that cool guy or girl and is tired of getting rejected. So the Eldar are kind of a**holes and the Tau are Cold War Commies arming and inciting Pro-Tau Insurgents and Rebels. Also the Imperium doesn't like it one bit, the ones that know about it that is.

Government To Do That lol: The Republic is as all Republics are, however more related to Rome than 'Murica, as a highly militaristic society, the right to vote is restricted to members, both active, reserved and retired, of the military, the Senate is responsible for the laws, and each senator is also a Lord General, one Lord General is elected by other generals to be Lord Regent of The Republic, with them their handpicked Lord Caesarian, the Senate is broken up into two major parties as well as a few minor ones, Their is the Republican Party, not related to the one you're thinking of, which is pro-independence and views The Imperium as a Looming threat, then there is the Imperial Party, I'm just great with these names aren't I, which, you guessed it, are all for fully joining the Imperium, minor parties include Pro Tau and individual Sub Sectors and planets that want independence. The Lord Regent holds a small council of appointed officials, similar to the High Lords of Terra in duty, as well as the aforementioned Lord Caesarian who is basically sent around The Republic Mass Effect style to make sure sh*t isn't falling apart at the seams.

Religion Joke: As mentioned earlier both Imperial religions are practiced to an extent, Missionaries from the Imperial Cult and their Sisters of Battle, were allowed to do their stuff as long as they didn't violence people to possible death, similar deal with the AdMech.

Those Other Bits Probably Worth Mentioning: As is every part of 40k there is always something sh*tty going on, so here are those bits, Orks are amok doing Ork things in the "Northern" part of the sector, Dark Eldar rave(raid) all over the "West" part of the sector raving things (other four-letter bad R word), Tau are spreading communism like a cheerleader at homecoming all over the "East" part of the sector, Necrons occasionally just 'happen', Tyranids generally exist here and there, Chaos doesn't normally happen, but when it does, it is a bit chaotic, The Imperium is going full Cold War all over the dam place, and internal politics suck more than that same cheerleader at the same homecoming.

So I hope that wasn't too bad, and like I said at the beginning any help would be appreciated.

The Imperium's policies toward integrating autonomous human's pre- Horus Heresy were a lot more lenient than they were after the Heresy, but they were still harsh by our standards.

Most expeditionary fleets seems to allow one chance for humans to surrender and once refused would force them into compliance. That compliance would be bitter and bloody. Even if human empires did give in and accept the Emperor as the master of humanity, they would be severely restricted in what they do as Xenos were seen as abhorrent (as declared by the Emperor).
Would your republic have had an STC as the basis for it's technology? That would lead to it's own issues.

Post Heresy this would have become even worse and then combine this with religious zeal of ecclesiarchy and the potential for the Mechanicum to strip the planet of interesting technology, I think you're slightly optimistic at the state of your republic.

Interestingly most systems would be semi-autonomous. It's more of a vassal relationship, where if the sector governors gives tithes, don't succumb to chaotic corruption and don't upset any of the many departments of the empire, then they get along fine and are left to govern how they want.
In most cases the brutal tithes (and fear of the punishment from not paying) would force the populace into destroying their own planet's ecosystem, or if they're an agriworld, just replacing their existing one with a more efficient food producing one. They would not be allowed to develop much new technology and individual rights and thought would be squashed as heresy.

A history of trading with aliens could lead to some interesting conflicts with both the imperium and tau, eldar etc. I can see the populace, having previously been independant, want to go back to their old ways as they see their planet plundered and destroyed in the name of this emperor who they've never seen.

I could see this working if the said republic was for some reason really difficult to reach, permanent warp storms etc.

I lightly glanced through http://wh40k.lexicanum.com/wiki/Imperial_Fists and apparently they did quite a bit in the Sol System during the 'Great Crusade' apparently. Seems like they had a few wars there and might have gone into other systems so you might want to pick one of those out. The 'Campaigns and Actions' section is what you might find interesting from that URL and you might get some ideas for yourself off that as to your location and name of planet etc to help fill out the location / planet maybes.

 Crimson wrote:
I could see this working if the said republic was for some reason really difficult to reach, permanent warp storms etc.

That'd work quite well. As long as they managed to get their tithes out... or were perhaps "forgotten" by the administratum or presumed destroyed.