more troublesome issue of "Southern Rights" arose within the Cherokee Nation. John Ross and the leadership of the Cherokee Nation struggled to maintain a position of neutrality, which was exceedingly difficult considering the location of the Cherokee Nation deep within the South and the proximity of "bleeding Kansas." However, in 1854 the Ross party lost votes to
an increasingly hard-line Southern-Rights party that believed an alliance with white southerners in the defense of slavery would be the best course for the nation. The pro slavery Southern Rights party was largely composed of those pro-assimilationist "Treaty Party" members who represented the elite ten-percent of the Nation. 
In 1855, Chief John Ross discovered the emergence of "a secret society organized in Delaware and Saline Districts" dedicated to the promotion of slavery and the removal of abolitionist interests from the Cherokee Nation.  Forming the core of this "sinister plot" were members of the so-called "Blue Lodges" (Freemasons) that had been organized by the Grand Lodge of Arkansas. The Grand Lodge of Arkansas was being used effectively in the promotion of the pro-Southern effort in Kansas and Oklahoma from Arkansas.  Many of the pro-slavery factions in the
Cherokee Nation had ties to Arkansas. John Ross, a Freemason himself, believed that these elements were spreading the pro-southern message among the "Blue Lodges" within the Cherokee Nation.
Some of the members of the "Blue Lodges" later formed the "Knights of the Golden Circle," an organization that
functioned somewhere in the blurred regions between Freemasonry and the Ku Klux Klan.  The Constitution of the Knights of the Golden Circle, as chartered on August 28, 1860 states:
"We, a part of the people of the Cherokee Nation, in order to form a more perfect union and protect ourselves and
property against the works of Abolitionists do establish this Constitution for the government of the Knights of the Golden Circle in this Nation...
"No person shall become a member of the Knights of the Golden Circle in the Cherokee Nation who is not a pro-slavery man...
The Captain, or in case of his refusal, then the Lieutenant has the power to compell each and every member of their encampments to turn out and assist in capturing and punishing any and all abolitionists in their minds who are interfering with slavery....
You do solemnly swear that you will keep all the secrets of this order and that you will, to the best of your abilities protect and defend the interests of the Knights of the Golden Circle in this Nation, so help you God." 
The leader of the Knights of the Golden Circle was Stand Watie, a Freemason, and members of the Knights of the Golden Circle included many of the elites of the Cherokee Nation, John Rollin Ridge; Elias Boudinot; William Penn Adair; James Bell -- all leaders of the Southern Rights party. "
"In July, a company of pro-Southern Cherokees led by Stand Watie attempted to raise the Confederate flag over the Cherokee Nation. Senator William Doublehead and 150 full-bloods confronted the Confederate Cherokees and bloodshed was only narrowly averted by the intervention of John Drew, a member of Chief John
Ross's family. 
On August 21, 1861, Chief John Ross addressed a meeting of some four thousand Cherokee meeting to discuss the Nation's stand in the coming Civil War and encouraged them to maintain neutrality: "the great object with me has been to have the Cherokee people's harmonious and united in the free exercise and enjoyment of all their rights of person and property. Union is strength; dissension is weakness, misery, ruin."  When the discussion was over, the Cherokee Nation had maintained its unity, but lost its neutrality. The Cherokee Nation became the last great nation to side with the Confederate States of America when it signed a treaty on October 7, 1861. 
Two Confederate regiments were raised by the Cherokee Nation. Brigadier General Ben McCulloch of the Confederate Army described them: "Colonel Drew's Regiment will be mostly full-bloods, whilst those with Col. Stand Watie will be half-breeds, and good soldiers anywhere, in or out of the Nation."  The membership in the two units fell directly upon party lines and membership in the corresponding secret societies. The largest part of the 1st Cherokee Mounted Rifles were members of the Keetoowah Society
and supporters of John Ross; most of the 2nd Cherokee Mounted Rifles were members of the Knights of the Golden Circle and followers of Colonel Stand Watie.  The leadership of both parties was composed of former Freemasons from Cherokee Lodge #21, Fort Gibson Lodge #35, and Flint Lodge #74. "
"By the time the war was over in 1866, seven thousand Cherokee had lost their lives; this amounted to from 1/4 to 1/3 of the Cherokee Nation.  No state suffered greater losses than did the Indian Territory in the Civil War.  General Stand Watie of the Knights of the Golden Circle was the last General of The Confederate States of America to surrender. With Watie's surrender, the Civil War within the Cherokee Nation was over."
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