Stand Watie learned to read and write English at a mission school in Georgia, and occasionally helped write for the Cherokee Phoenix newspaper, which led him into the dispute over the Georgia state repressive anti-Indian laws. Later, when gold was discovered on Cherokee lands in northern Georgia, thousands of white settlers encroached on Indian lands. In spite of federal treaties protecting Indians from state actions, in 1832 Georgia confiscated most of the Cherokee land and the Georgia militia destroyed the Cherokee Phoenix.
The Watie brothers stood in favor of the Removal of the Cherokee to Oklahoma and were members of the Ridge Party that signed the Treaty of New Echota. The anti-Removal Ross Party (elected democratically by the majority) refused to ratify it. Watie, his family, and many other Cherokees emigrated to the West. Those Cherokees (and their slaves) who remained on tribal lands in the East were forcibly removed by the U.S. government in 1838 in a journey known as the "Trail of Tears," during which thousands died. The Ross Party targeted Stand and Buck Watie and the Ridge family for assassination and, of the four men mentioned above, only Stand Watie managed to escape with his life.
Watie, a slave holder, started a successful plantation on Spavinaw Creek in the Indian Territory. He served on the Cherokee Council from 1845 to 1861, serving part of that time as speaker.
After Chief John Ross and the Cherokee Council decided to support the Confederacy, Watie organized a regiment of cavalry. In October 1861, he was commissioned as colonel in the First Cherokee Mounted Rifles. Although he fought Federal troops, he also led his men in fighting between factions of the Cherokee, as well as against the Creek and Seminole and others who chose to support the Union. Watie is noted for his role in the Battle of Pea Ridge, Arkansas, a Union victory, on March 6–8, 1862. Watie's troops captured Union artillery positions and covered the retreat of Confederate forces from the battlefield.
After Cherokee support for the Confederacy fractured, Watie continued to lead the remnant of his cavalry. He was promoted to brigadier general by General Samuel Bell Maxey, and was given the command of the First Indian Brigade, composed of two regiments of Mounted Rifles and three battalions of Cherokee, Seminole and Osage infantry. These troops were based south of the Canadian River, and periodically crossed the river into Union territory. They fought in a number of battles and skirmishes in the western Confederate states, including the Indian Territory, Arkansas, Missouri, Kansas, and Texas. Watie's force reportedly fought in more battles west of the Mississippi River than any other unit.
During the war General Watie's family remained with other Confederate and former Ridge Party Cherokees in Rusk and Smith Counties of east Texas. This community known at times as the Mount Tabor Community and also by the town name of Bellview, Texas, allowed warriors to stay out on campaigns, knowing that their wives and children were in relative safety. Although hardships in east Texas did exist, this knowledge helped form the Cherokee and allied warriors into the potent Confederate fighting force that held Union troops out of southern Indian Territory and large parts of north Texas throughout the war.
On June 23, 1865, at Fort Towson in the Choctaw Nation's area of the Indian Territory, Watie signed a cease-fire agreement with Union representatives, becoming the last Confederate general in the field to stand down.