Short answers, pulled from the story.
Chief John Ross insisted upon the nation's neutrality when the war broke out. He remained a Union advocate throughout the conflict despite pressure from other factions.
Stand Watie officially became the last Confederate general to end fighting on the 25th of June 1865 at Fort Towson. This location sat in the southeast portion of the Indian Territory.
The Cherokee Nation had approximately 21,000 members with 3,000 serving as soldiers. These individuals operated primarily Native Confederate units under Watie's command.
The Cherokee aligned with the Confederacy partly due to existing cultural affinities and trading ties connected to states that had seceded. Mixed-blooded Cherokee supported the three-quarters Cherokee Stand Watie because they were largely English-speaking assimilationists and slaveholding aristocracy.
The eastern Cherokee faced a severe smallpox outbreak following the war while Thomas and many followers remained deeply in debt. The federal government recognized the eastern tribe as separate from the western tribe and they filed a lawsuit against the Cherokee's creditors leaving protection to the federal government.