Here's an excerpt from http://www.tolatsga.org/Cherokee2.html that provides some background information about the Cherokees:

"...On the eve of the Civil War in 1861, the Cherokee Nation was controlled by a wealthy, mixed-blood minority which owned black slaves and favored the South. The vast majority of the Cherokee did not have slaves, lived simple lives and could have cared less about the white man's war, especially the Old Settlers. John Ross leaned towards the South, but mindful of the divisions within the Cherokee, refused the early offers by Albert Pike to join the Confederacy. When Union soldiers withdrew during the summer of 1861, the Confederate army occupied the Indian Territory. The Cherokee Nation voted to secede from the United States in August, 1861, and a formal treaty was signed at the Park Hill home of John Ross between the Cherokee Nation and the new Confederate government. Four years later, this agreement was to cost them very dearly.

Americans are usually surprised to learn that the Civil War was bitterly contested between the Native Americans in Oklahoma. For the Cherokee, it was very much a war of brother against brother. 3,000 Cherokee (usually New Settlers) enlisted in the Confederate army while 1,000(Old Settlers) fought for the Union. In the east 400 North Carolina Cherokee, virtually every able bodied man, served the South. Cherokee Civil War Units included: First Cherokee Mounted Rifles (First Arkansas Cherokee); First Cherokee Mounted Volunteer (Watie's Regiment, Cherokee Mounted Volunteers); Second Regiment, Cherokee Mounted Rifles, Arkansas; First Regiment, Cherokee Mounted Riflemen; First Squadron, Cherokee Mounted Volunteers (Holt's Squadron); Second Cherokee Mounted Volunteers (Second Regiment,Cherokee Mounted Rifles or Riflemen); and Cherokee Regiment(Special Service).

Cherokee units fought at Wilson Creek (1861) and Pea Ridge (1862). There were few large battles in Oklahoma, but these were brutal. In November 1861, a combined force of 1,400 Cherokee, Chickasaw, Choctaw, and Texas cavalry commanded by Colonel Douglas Cooper attacked a refugee column of 4,000 pro-Union Creek trying to reach safety in Kansas. Over 700 refugees were killed during the three day battle before reason took hold. After two assaults against the Creek, the Cherokee refused to participate in a third and withdrew. Meanwhile the Cherokee allegiance to the Confederacy faltered. Following the Confederate defeat at Pea Ridge, John Ross switched sides to the Union. Actually Ross allowed himself to be captured in 1862 and spent the rest of the war in Philadelphia. John Drew's Mounted Rifle regiment also deserted and was reorganized as a regiment in the Union army, but other Cherokee units under Stand Watie remained loyal to the Confederacy.

The fighting in Oklahoma degenerated into the same vicious guerilla warfare that prevailed among the white settlers of Kansas and Missouri. Stand Watie, who became a Confederate general, was a leader of the Treaty Party and personally hated John Ross. After Ross switched in 1862 and went east, Stand Watie was elected principal chief of the Cherokee Nation in August. He captured the Cherokee capital at Tahlequah and ordered Ross' home burned. The fighting produced hatreds that, added to the earlier differences, endured long after the war was over. Many Oklahoma Indians fled north to escape the fighting. Kansas eventually had more than 7,000 refugees from the Indian Territory which it could not house or feed. Many froze to death or starved. Heavily involved in the fighting throughout the war, the Cherokee Nation lost more than 1/3 of its population. No state, north or south, even came close to this. On June 23, 1865, Stand Watie was the last Confederate general to surrender his command to the United States.

Afterwards, the victorious federal government remembered the services of General Stand Watie to the Confederacy. It also remembered the 1861 vote by the Cherokee legislature to secede from the United States. These provided the excuse to invalidate all previous treaties between the Cherokee and United States. John Ross died in 1866, and in new treaties imposed in 1866 and 1868, large sections of Cherokee lands were taken for railroad construction, white settlement (1889), or the relocation of other tribes. The Cherokee Nation never recovered to the prosperity it had enjoyed before the Civil War. As railroads were built across Cherokee lands, outlaws discovered that the Indian territory, especially the Cherokee Nation, was a sanctuary from federal and state laws. Impoverished by the war, the Cherokee also began to lease lands to white tenant farmers. By 1880, whites outnumbered the Indians in the Indian Territory.

In 1885 a well-intentioned, but ill-informed, Senator Henry Dawes of Massachusetts decided that holding of land in common was delaying the progress of Indians towards "civilization." Forming an alliance with western Congressmen who wish to exploit Indian treaty lands, he secured passage of the General Allotment(Dawes) Act in 1887 which ultimately cost Native Americans 2/3 of their remaining land base. The Five Civilized Tribes of Oklahoma were exempt from allotment, but came under tremendous pressure to accept it. Until the 1880s, cattle from the Chisholm and Texas trails routinely grazed on the lands of the Cherokee Outlet before going to the Kansas railheads. The Cherokee earned a good income from this enterprise until it was halted without explanation by the Commissioner of Indian Affairs in 1890. It should also be noted that the Oklahoma Territory was organized that same year from the western half of the Indian Territory, and there may have been some connection! After the Cherokee were forced to sell, the land was made available for white settlement.

The Dawes commission attempted to get the Five Tribes to accept allotment in 1893, but they refused. This led to the passage of the Curtis Act (1895) which dissolved tribal governments and forced allotment during 1901. Grafting(swindles) of Indian lands became a massive and unofficially sanctioned form of theft in Oklahoma. Of the original seven million acres granted the Cherokee in the New Echota Treaty, the Cherokee Nation kept less than 1/3 of 1 percent. As compensation, the Cherokee became citizens in 1901 and were finally allowed to vote. An attempt by the Five Tribes to form their own state of Sequoyah in eastern Oklahoma failed in 1905, and the Cherokee Nation was officially dissolved on March 3, 1906. The following year Oklahoma was admitted as the 46th state. The present government of the Cherokee Nation was formed in 1948 after passage of the Wheeler-Howard Indian Reorganization Act (1934). In 1961 the Cherokee Nation was awarded $15,000,000 by the U.S. Claims Commission for lands of the Cherokee Outlet."