During the first six months of 1862, the Indian Territory saw but little of the war, though Confederate troops were stationed at Fort Gibson, Fort Washita and elsewhere. In the middle of the summer of that year, however, there was an invasion of Federal forces into the Cherokee Nation from Kansas, under the command of Colonel William Weer. It advanced far enough to send scouting parties to Tahlequah and Fort Gibson but, because of the lack of proper discipline among some of the leading officers of the command, it soon retreated northward into Kansas. Many of the Cherokee people declared their adherence to the Union at this time and three regiments of Indians (Cherokees, Creeks and Seminoles) were organized for the Federal service.
In October, 1862, occurred the second Federal invasion of the Cherokee Nation. General James G. Blunt was in command of the Federal forces. Fort Gibson was again abandoned by the Confederate forces and was occupied by the Federal troops. It continued to be the headquarters for the Union troops in the Indian Territory from that time on until the end of the war. Most of the Confederate forces in the Indian Territory were stationed in the Chickasaw and Choctaw nations thereafter, though there were frequent raids northward into the Creek and Cherokee nations. Probably the most important battle fought in the Indian Territory during the Civil War was that of Elk Creek, or Honey Springs, near the present town of Oktaha, in the southern part of Muskogee County, in July, 1863, between the Union troops under the command of General Blunt and the Confederate forces under the command of General Blunt and the Confederate forces under the command of General William Steele and General Douglas H. Cooper. It resulted in a victory for the Union forces, the Confederate troops retreating southward across the Canadian River.
The war was bitterly partisan. Raiding parties from both sides scoured the country in the Cerokee and Creek nations, destroying the property and driving off the stock of all who were on the opposite side, so that the whole country was laid waste. The families of those who sided with the Confederate States had to seek refuge in the southern part of the Choctaw and Chickasaw naitons, while the families of those who sided with the Union were mostly gathered in and around Fort Gibson and the southern part of Kansas. Living in idleness, in overcrowded camps, poorly clothed, poorly housed and exposed to the ravages of disease, there were many deaths among the people on both sides. There were no more battles of importance in the Territory during the Civil War, though there were numerous skirmishes and small fights between raiding parties. In September, 1864, a Confederate force of 2,000 men under Generals Stand Watie and Richard M. Gano, captured a Federal supply train of 325 wagons, at Cabin Creek, in the northeastern part of Mayes County, near the town of Pensacola. During the last six months of the Civil War, there was practically no campaigning done in the Indian Territory. When the war ended, General Cooper, who was in command of all the Confederate troops in the Territory, surrendered the white troops, those of the regiment from Texas and the other states, but the Indians reserved the right to do their own surrendering. The Cherokee and Choctaw troops in the Confederate service were surrendered in June, 1865, and the Chickasaw troops were not surrendered until July 14th, more than three months after the surrender of General Lee's army.
The Civil War was one in which the Indians were not directly concerned and in which but few of them would have taken part had they not been subject to much persuasion. It was disastrous to them in every way. Most of their property was destroyed and many of them lost their lives and, in the end, much of their land was also taken from them. Of course, all of their slaves were set free, but that was a small matter compared with the other losses sustained and with the hardships which they endured.
