For the Cherokee, the conflict pitted brother against brother.
The Civil War not only split the United States, but it also tore apart various Indian tribes. The Cherokee were deeply affected. Most supported the Confederacy, and many joined the 1st Cherokee Mounted Rifles. But a significant number of Cherokee supported the Union.
So while the Mounted Rifles engaged Union troops on a few occasions, they spent most of their time attacking other Cherokees, as well as Seminoles and Creeks. The split lasted for decades, even after the war had come to an end.