Both the "Western Cherokees" and the "Eastern Cherokees" objected to the Treaty of New Echota, stating that the signers had not been authorized. However, the Western Cherokees sent two delegates, James Rogers and John Smith to make sure the provisions in the treaty were clear about the position the Cherokee Nation would have when arriving in Western Cherokee territory. The provision in the treaty, signed by the two Keetoowahs, assured the Cherokee Nation of a friendly disposition of their people and their desire that the nation should be united again as one people. That Uniting was meant to be with the Cherokee Nation joining the Western Cherokee government. The provision assured them “a hearty welcome and an equal participation with them in all the benefits and privileges of the Cherokee country west.” The provision concluded with, “But it is expressly understood that nothing in this treaty shall affect any clams of the Western Cherokees on the United States.” (Treaty of New Echota, December 31, 1835, 7 Stat, 487) .

The Western Cherokees gave welcome to their friends and family without complaint; they said there was room enough for all. The Cherokee Nation council marked off a public square in the new capital of Tahlequah, and surrounded it with a rail fence and erected a log cabin for its headquarters, even though the Western Cherokees had already organized their governmental system, and made treaties in the west separate from the old Cherokee Nation. The stipulation in the Treaty of New Echota was ignored, mainly because the old Cherokee Nation considered the entire treaty invalid.

The administration of the Western Cherokee felt very strongly about the issue of governance, and in early June, 1839, the Western Chiefs called some six thousand Cherokees together for a three-week convention. They met in their new Keetoowah council house at Takatoka, north of Tahlequah. The new Western Cherokee Chief, John Brown, graciously welcomed the newcomers. The Cherokee newcomers were told they were welcomed, could vote in future elections, and were even eligible for political office. But at the same time, they would be subject to the laws of the Western Cherokee. However, John Ross and his administration were ready. They presented a list of written resolutions calling for the formation of a new Cherokee Nation west of the Mississippi. They suggested the council be made up of an equal number of Old Settlers and old Cherokee Nation representatives. Brown reminded them that a government already existed. (Brown, Looney and Rogers letter, June 19, 1839, Letters Received, OIA, Cherokee Agency (M-234), NA; Starr History 110-11) Due to majority and aggression, the old Cherokee Nation moved to eventually coerce some Western Cherokees to sign an Act of Union at Tahlequah, joining the two governments and putting Ross in charge. This was never ratified by the Western Cherokees, or accepted by the U.S. Government. The Western Cherokees treaties were not changed.

Tahlonteeskee was discontinued as the capital, and for a while the capital was at Takatoka Council house, north of Tahlequah. It was eventually moved to Tahlequah. For a brief time in the 1860's, it was proposed that the capital move to the town of Keetoowah, located at what is now Fort Gibson. Tahlonteeskee continued to be a meeting place, and eventually became the 'seat' of the Cherokee Nation district, "Illinois." The arrival of the Cherokee Nation to Indian Territory brought a power struggle between the larger Cherokee Nation and Old Settler, Western Cherokee Keetoowahs, who had prior claim to the territory. The Treaty of 1846 forced the two groups to combine until the Civil War.

Many of the Western Cherokees saw the approaching Civil War as inevitable, and perceived it as a threat to traditional Kituwah culture. They also acknowledged that the Cherokees were still divided into two main factions, with their faction being the minority. The Keetoowahs, as did most full-bloods who did not own slaves, sided with the Union (Wright, A Guide to the Indian Tribes of Oklahoma, p.70) Following the guidance of several non-Indian missionaries, the Keetoowah's adopted a constitution in 1859, calling itself the "Keetoowah Society." The original object of the Society was to maintain and assert the rights of all the Cherokee people or the Cherokee Nation under the laws and treaties with the government of the United States, and in fact today it is still asserting those rights as the United Keetoowah Band of Cherokee Indians in Oklahoma. Some of these rights are religious, some are property, and some political. James Duncan, English Secretary of the Society in 1926, stated, "As to property rights, perhaps of more importance to the Cherokees than political, many do not know and realize that the Society has, in a number of instances, 'saved the day.' (Chronicles of Oklahoma, 1926)

On April 15, 1858, a small number of leading members of Keetoowahs got together and discussed the affairs of the Cherokees, the purpose and objectives for which they had always stood. They discussed what the final result probably would be caused by the existing state of affairs in the United States. The people of the United States were divided and it was clear they were about to fight. The Cherokees were situated too far in the South and the men were becoming reckless and seemed to be taking sides with the South, but the leading cause was those who owned negro slaves. It was plain to be seen that Cherokee people without a full understanding were taking sides with the South. It was plain the teachers from the North were objected to and were being forced out of the Cherokee Nation. They believed if the Missionaries were gone all the Cherokee people would go to the side of the South, but they were mistaken. These matters were already understood by the Keetoowahs, and the Keetoowahs felt sure what the final result would be. They knew the relative members of the several states. It seemed certain that the states of the South were entering into a conspiracy to abandon the union of states to set up a separate government. (Keetoowah Laws - April 29, 1859)

The old people say that the Kituwah people sided with the north, also because they did not want the states and people who had stolen their land and homes to be a power they would have to resume negotiating with. In 1859, the Keetoowahs wrote that the South are the people who took our lands away from us which lands the Creator had given to us, where our forefathers were raised.

A meeting of the Keetoowahs took place April 20, 1858. (ibid) Bud Gritts was appointed to create a plan that would be best for the Cherokee people and place the Keetoowah in charge of the Cherokee government at large. All Cherokee people in all the districts were informed, and it was accepted all over by the confidential Keetoowah lodges. (ibid) A formal convention was held the following year, and it was adopted on April 29, 1859.

Today, some people say this was the beginning of the Keetoowah Society, but it is clear from the words stated in their documents that their forefathers had always been Keetoowah. This was merely a reorganization, which constituted a written document, instigated by white missionaries who presented this option to the Keetoowahs for the first time. Rolls were taken of Keetoowahs in each district (lodges).

The Civil War brought renewed conflict. The Keetoowah full bloods were non-slaveholders and fought for the Union. The Keetoowahs became known also as "Pin Indians" or "Pins." After the war, the U.S. Government refused to treat the Keetoowahs as allies, forcing them the same penalties as were given to the Cherokee Nation. During 1865 and 1866, the combined governments of the Cherokee Nation signed two treaties with the U.S. government. This lasted until 1898 when the pressure for allotment became great.

Tensions continued through the years, between the Cherokee Nation proper and the Keetoowahs. Schools set up by the Cherokee Nation newcomers actually intensified differences between the two groups. "Since there were few qualified Cherokee-speaking teachers, many of the schools were staffed by whites who spoke no Cherokee. Children of full blood families found it frustrating and humiliating to go to school when they couldn't understand their teacher, and were ridiculed by class mates. Consequently, it was predominantly the sons and daughters of mixed-bloods who attended schools, although over two-thirds of the Cherokees were full bloods." (Indian Territory on the Eve of Civil War, Brad Agnew, p. 36) A far cry from when Sequoyah was supervising the Keetoowah schools.