On the reorganization of the united Nation the council ground at Tahlequah was designated as the seat of government, and the present town was soon afterward laid out upon the spot, taking its name from the old Cherokee town of Tălikwă′, or Tellico, in Tennessee. The missions were reestablished, the Advocate was revived, and the work of civilization was again taken up, though under great difficulties, as continued removals and persecutions, with the awful suffering and mortality of the last great emigration, had impoverished and more than decimated the Nation and worn out the courage even of the bravest. The bitterness engendered by the New Echota treaty led to a series of murders and assassinations and other acts of outlawry, amounting almost to civil war between the Ross and Ridge factions, until the Government was at last obliged to interfere. The Old Settlers also had their grievances and complaints against the newcomers, so that the history of the Cherokee Nation for the next twenty years is largely a chronicle of factional quarrels, through which civilization and every good work actually retrograded behind the condition of a generation earlier.

Sequoya, who had occupied a prominent position in the affairs of the Old Settlers and assisted much in the reorganization of the Nation, had become seized with a desire to make linguistic investigations among the remote tribes, very probably with a view of devising a universal Indian alphabet. His mind dwelt also on the old tradition of a lost band of Cherokee living somewhere toward the western mountains. In 1841 and 1842, with a few Cherokee companions and with his provisions and papers loaded in an ox cart, he made several journeys into the West, received everywhere with kindness by even the wildest tribes. Disappointed in his philologic results, he started out in 1843 in quest of the lost Cherokee, who were believed to be somewhere in northern Mexico, but, being now an old man and worn out by hardship, he sank under the effort and died—alone and unattended, it is said—near the village of San Fernando, Mexico, in August of that year. Rumors having come of his helpless condition, a party had been sent out from the Nation to bring him back, but arrived too late to find him alive. A pension of three hundred dollars, previously voted to him by the Nation, was continued to his widow—the only literary pension in the United States. Besides a wife he left two sons and a daughter.[370] Sequoyah district of the Cherokee Nation was named in his honor, and the great trees of California (Sequoia gigantea) also preserve his memory.

In 1846 a treaty was concluded at Washington by which the conflicting claims of the Old Settlers and later emigrants were adjusted, reimbursement was promised for sums unjustly deducted from the five-million-dollar payment guaranteed under the treaty of 1835, and a general amnesty was proclaimed for all past offenses within the Nation.[371] Final settlement of the treaty claims has not yet been made, and the matter is still a subject of litigation, including all the treaties and agreements up to the present date.

In 1859 the devoted missionary Samuel Worcester, author of numerous translations and first organizer of the Advocate, died at Park Hill mission, in the Cherokee Nation, after thirty-five years spent in the service of the Cherokee, having suffered chains, imprisonment, and exile for their sake.[372]

The breaking out of the civil war in 1861 found the Cherokee divided in sentiment. Being slave owners, like the other Indians removed from the southern states, and surrounded by southern influences, the agents in charge being themselves southern sympathizers, a considerable party in each of the tribes was disposed to take active part with the Confederacy. The old Ridge party, headed by Stand Watie and supported by the secret secession organization known as the Knights of the Golden Circle, declared for the Confederacy. The National party, headed by John Ross and supported by the patriotic organization known as the Kitoowah society—whose members were afterward known as Pin Indians—declared for strict neutrality. At last, however, the pressure became too strong to be resisted, and on October 7, 1861, a treaty was concluded at Tahlequah, with General Albert Pike, commissioner for the Confederate states, by which the Cherokee Nation cast its lot with the Confederacy, as the Creeks, Choctaw, Chickasaw, Seminole, Osage, Comanche, and several smaller tribes had already done.[373]

Two Cherokee regiments were raised for the Confederate service, under command of Stand Watie and Colonel Drew, respectively, the former being commissioned as brigadier-general. They participated in several engagements, chief among them being the battle of Pea Ridge, Arkansas, on March 7, 1862.[374] In the following summer the Union forces entered the Cherokee country and sent a proposition to Ross, urging him to repudiate the treaty with the Confederate states, but the offer was indignantly declined. Shortly afterward, however, the men of Drew’s regiment, finding themselves unpaid and generally neglected by their allies, went over almost in a body to the Union side, thus compelling Ross to make an arrangement with the Union commander, Colonel Weir. Leaving the Cherokee country, Ross retired to Philadelphia, from which he did not return until the close of the war.[375] In the meantime Indian Territory was ravaged alternately by contending factions and armed bodies, and thousands of loyal fugitives were obliged to take refuge in Kansas, where they were cared for by the government. Among these, at the close of 1862, were two thousand Cherokee. In the following spring they were sent back to their homes under armed escort to give them an opportunity to put in a crop, seeds and tools being furnished for the purpose, but had hardly begun work when they were forced to retire by the approach of Stand Watie and his regiment of Confederate Cherokee, estimated at seven hundred men. Stand Watie and his men, with the Confederate Creeks and others, scoured the country at will, destroying or carrying off everything belonging to the loyal Cherokee, who had now, to the number of nearly seven thousand, taken refuge at Fort Gibson. Refusing to take sides against a government which was still unable to protect them, they were forced to see all the prosperous accumulations of twenty years of industry swept off in this guerrilla warfare. In stock alone their losses were estimated at more than 300,000 head.[376]

“The events of the war brought to them more of desolation and ruin than perhaps to any other community. Raided and sacked alternately, not only by the Confederate and Union forces, but by the vindictive ferocity and hate of their own factional divisions, their country became a blackened and desolate waste. Driven from comfortable homes, exposed to want, misery, and the elements, they perished like sheep in a snow storm. Their houses, fences, and other improvements were burned, their orchards destroyed, their flocks and herds slaughtered or driven off, their schools broken up, their schoolhouses given to the flames, and their churches and public buildings subjected to a similar fate; and that entire portion of their country which had been occupied by their settlements was distinguishable from the virgin prairie only by the scorched and blackened chimneys and the plowed but now neglected fields.”[377]

After five years of desolation the Cherokee emerged from the war with their numbers reduced from 21,000 to 14,000,[378] and their whole country in ashes. On July 19, 1866, by a treaty concluded at Tahlequah, the nation was received back into the protection of the United States, a general amnesty was proclaimed, and all confiscations on account of the war prohibited; slavery was abolished without compensation to former owners, and all negroes residing within the Nation were admitted to full Cherokee citizenship. By articles 15 and 16 permission was given the United States to settle friendly Indians within the Cherokee home country or the Cherokee strip by consent and purchase from the Nation. By article 17 the Cherokee sold the 800,000-acre tract in Kansas secured by the treaty of 1835, together with a two-mile strip running along the southern border of Kansas, and thereafter to be included within the limits of that state, thus leaving the Cherokee country as it was before the recent cession of the Cherokee strip. Payment was promised for spoliations by United States troops during the war; and $3,000 were to be paid out of the Cherokee funds to the Reverend Evan Jones, then disabled and in poverty, as a reward for forty years of faithful missionary labors. By article 26 “the United States guarantee to the Cherokees the quiet and peaceable possession of their country and protection against domestic feuds and insurrection as well as hostilities of other tribes. They shall also be protected from intrusion by all unauthorized citizens of the United States attempting to settle on their lands or reside in their territory.”[379]

The missionary, Reverend Evan Jones, who had followed the Cherokee into exile, and his son, John B. Jones, had been admitted to Cherokee citizenship the year before by vote of the Nation. The act conferring this recognition recites that “we do bear witness that they have done their work well.”[380]

John Ross, now an old man, had been unable to attend this treaty, being present at the time in Washington on business for his people. Before its ratification he died in that city on August 1, 1866, at the age of seventy-seven years, fifty-seven of which had been given to the service of his Nation. No finer panegyric was ever pronounced than the memorial resolution passed by the Cherokee Nation on learning of his death.[381] Notwithstanding repeated attempts to subvert his authority, his people had remained steadfast in their fidelity to him, and he died, as he had lived for nearly forty years, the officially recognized chief of the Nation. With repeated opportunities to enrich himself at the expense of his tribe, he died a poor man. His body was brought back and interred in the territory of the Nation. In remembrance of the great chief one of the nine districts of the Cherokee Nation has been called by his Indian name, Cooweescoowee (46).