In the spring of 1863 the United States army chiefs in Kansas decided to occupy the Cherokee country and as much of the rest of the Indian Territory as possible, in order to permit the refugees to return to their homes. The Cherokee council's repudiation of the alliance with the Confederacy had changed very considerably the situation of the Cherokee Nation, but the activity of the forces still adhering to the South made the return of the refugees impossible without military protection.

During the late winter and early spring Colonel W. A. Phillips of the Union army carried on aggressive operations in the northern part of the Cherokee country; a little later he moved south with a strong force a little later he moved south with a strong force and occupied Fort Gibson. From this south with a strong force and occupied Fort Gibson. From this post he sent out raiding expeditions and also sought to protect the northern refugees who returned to their homes. In the latter attempt he met with only fair success. Stand Watie and other Cherokee leaders, who were very active at this time, carried on counter-raids so that there was little safety for the returned civilian population unless they remained in or very near Fort Gibson. The activity of Phillips, however, coupled with reprisals from the returning refugees, drove the southern Indian civilians south to camps along the Red River or into Texas. With some ten thousand Cherokees now aligned with the north, and with nearly seven thousand still adhering firmly to the South, the Cherokee Nation was virtually engaged in a small civil war of its own. The results were disastrous. Elias C. Boudinot, son of the elder Boudinot, had been elected delegate to the Confederate Congress at Richmond. He strove earnestly and with some success to obtain money from the government of the Confederacy to feed the starving refugees along the Red River and to supply arms and equipment to the Cherokee soldiery fighting for the southern cause. But it was not to be, and the refugees on the Red River became even more destitute than their counterparts had been in Kansas.

The Civil War in Indian Territory