Short answers, pulled from the story.
The Five Civilized Tribes including Cherokee, Chickasaw, Choctaw, Creek, and Seminole nations aligned with the Confederacy. At least 7,860 Native Americans from Indian Territory served as officers and enlisted men in the Confederate Army.
The first battle occurred on the 19th of November 1861 at Deep Fork. This engagement involved Opothleyahola rallying 7,000 people against a force of 1,400 Confederate soldiers under Colonel Douglas H. Cooper.
General Stand Watie officially became the last Confederate general to surrender on the 25th of June 1865 at Fort Towson in Choctaw lands. He surrendered along with his troops at Doaksville which marked the end of major conventional fighting in the region.
Reconstruction Treaties forced land concessions upon the tribes and required Cherokee and other nations to emancipate their slaves. Later issues arose when American Indian lands were allotted under the Dawes Commission between 1902 and 1906.