An American Genghis Khan.

That seems to be one of the bigger issues. How do I get, say, the Dakota Sioux, to not only form an alliance among the tribes in it's area, but also actually get them to willingly begin a battle of unification with tribes that have been their long time enemies? There are many tribes (Crow, Shoshone) that willingly joined in battle against the Sioux and others on the side of the American Army because they had hated the Sioux (and others) for so much longer!
I'm also wondering if I'm going to need a Maverick Brit that will work with 'Genghis' to funnel guns and powder to the tribes.

Someone a la Lawrence of Arabia but for the plains Indians ?
 
I'm unsure about how you feel about PoDs, as it sounds like you want a PoD that still keeps the US and etc. Let's ditch Columbus at the door and get some other PODs. Serbs get a little more lucky, and don't immediately spiral apart when Stefan Dusan dies. They, along with a Timur-descendant coming along every few decades, nerf the Ottomans and keep Italians and other Christians in the markets of the Middle East. Portugal is content hugging the African coast selling slaves to the Barbary states, and Spain gets busy trying to conquer North Africa. All the while, as the North Sea fisheries come under intense exploitation, some entrepreneurial whalers and fishermen sailing far to the West encounter some strange lands with strange people. They are however, still people and they start trading fish, furs, vegetables, and tools. Some Europeans even stay around with the Natives, prepping the place for the next time a ship arrives. Horses, sheep, cattle, beets, and clover are all brought over to build a small sailor's paradise. Europe is relatively unaffected, with most ships never stopping in the new lands except for some supplies and good times. One spring, as a ship arrives, the villages they'd expect a welcome from are emptied, and when they begin to explore, discovery of infected individuals drives the ship away. European ships still pilot the North Atlantic, but many are wary of what may lie in those mysterious western lands. Most European sovereigns are busy elsewhere, often involved more in some lucrative Eastern Mediterranean trade voyages and the Baltic.

Meanwhile in the Americas, hell breaks loose, as smallpox races down the St. Lawrence valley to the Great Lakes, soon reaching the remnants of the Mississippians. Violence, warfare, and chaos intensify as disease rips society apart. Migrations are kicked off as populations move to flee disease. By the middle of the 1550s, epidemics have reached the border of the Mesoamerican region. The 1560s would see European diseases meet the Inca. Following, not too quickly in their wake are the other flora and fauna. By around 1560, Horses have reached the border of the Great Plains through starved wanderers and traded animals. It's not long before they become steeds to various Mississippi remnants looking for a technological edge over their contemporaries. As many southern Mississippi groups stayed settled, it was the descendants of the Northerners who were left at the edge of the recovering Mississippian economy who began taking up the horse as an exclusive source of wealth. The Horseback Revolution takes place not only earlier, with less European interference, but also enters North America from the North to the South.

With these epidemics and an uncharacteristically high rainfall from 1570-1600, the Bison population explodes ridiculously, with individuals going as far east as the Atlantic Ocean. Armed with horses early, Eastern peoples like the Omaha, Dakota etc. take to extreme amounts of buffalo hunting, producing pemmican on an industrial scale, and trading it for weapons, tools, and ceramics. As the Southern Mississippi remnants like the Caddoan and Creek settle down, the slave trade resumes, providing another source of income for the Plains Indians. Eventually one group grows more powerful than the others, with steady access to weaponry, bison, and trade and wages war to dominate the other plains groups. It is in this environment a particularly savvy, lucky, or otherwise exceptional individual forges an empire dominating the pemmican and Plains slave trade.

viola
 
For a core of an American Khanate, maybe the Cherokee? They had cordial-enough relations with most other tribes that weren't the Catawba.
 
Not sure if a post industrial khanate is possible at all no matter if GB is bankrolling them or not. Everything is too different. You need a PoD in the 18th century or earlier period.
 
To be clear, are you envisioning all Native American tribes uniting under one ruler? Like the tribes of the Northwest, Great Plains and Southwest banding together?
Did tribes like Apache had knowledge about Siox and Cheyenne during the 19th Century for example ? I always wondered that. The Comanche migrated very far so they must have contacted numerous tribes of different areas.
 
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