In spite of the alliance, many Cherokee had no affection for the Southern States who had forced them from their homeland in the East. In December, many of the full bloods in Col. John Drew's 1st Cherokee Mtd Rifles had deserted to avoid fighting against Opothleyahola's Loyal Creeks on their exodus to Kansas.
In July 1862, Union troops occupied the capital city of Tahlequah and, after some negotiation, Chief Ross was voluntarily captured. In August 1862, The Southern Cherokee elected Stand Watie as their Principal Chief.
Ross traveled to Washington to try to convince President Lincoln that the Confederate Treaty was signed under duress and the majority of Cherokee were loyal to the Union. The National Council rescinded the Confederate Treaty and emancipated slaves in the Cherokee Nation. However, it was another year before Federal Troops effectively controlled the Cherokee Nation.
The Nation was essentially a no-man's land. While thousands of Loyal Cherokee refugees were starving in Kansas, the families of the Southern Cherokee were refugees in Texas and Arkansas.Cherokee Neutrality