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Native Americans

Lincoln's relationship with Native Americans started before he was born, with their killing of his grandfather in front of his sons, including Lincoln's father Thomas. Lincoln himself served as a captain in the state militia during the Black Hawk War but saw no combat. Lincoln used appointments to the Indian Bureau as a reward to supporters from Minnesota and Wisconsin. While in office his administration faced difficulties guarding Western settlers, railroads, and telegraphs, from Indian attacks.

On August 17, 1862, the Dakota War broke out in Minnesota. Hundreds of settlers were killed, 30,000 were displaced from their homes, and Washington was deeply alarmed. Some feared incorrectly that it might represent a Confederate conspiracy to start a war on the Northwestern frontier. Lincoln ordered thousands of Confederate prisoners of war sent by railroad to put down the uprising. When the Confederates protested forcing Confederate prisoners to fight Indians, Lincoln revoked the policy and none arrived in Minnesota. Lincoln sent General John Pope as commander of the new Department of the Northwest two weeks into the hostilities. Before he arrived, the Fond Du Lac band of Chippewa sent Lincoln a letter asking to go to war for the United States against the Sioux, so Lincoln could send Minnesota's troops to fight the South. Shortly after, a Mille Lacs Band Chief offered the same at St. Cloud, Minnesota. In it the Chippewa specified they wanted to use the indigenous rules of warfare. That meant there would be no prisoners of war, no surrender, no peace agreement. Lincoln did not accept the Chippewa offer, as he could not control the Chippewa, and women and children were considered legitimate casualties in native American warfare.

Serving under Gen. Pope was Minnesota Congressman Henry H. Sibley. Minnesota's Governor had made Sibley a Colonel United States Volunteers to command the U.S. force tasked with fighting the war and that eventually defeated Little Crow 's forces at the Battle of Wood Lake. The day the Mdewakanton force surrendered at Camp Release, a Chippewa war council met at Minnesota's capitol with another Chippewa offer to Lincoln, to fight the Sioux. Sibley ordered a military commission to review the actions of the captured, to try those that had committed war crimes. The legitimacy of military commissions trying opposing combatants had been established during the Mexican War. Sibley thought he had 16-20 of the men he wanted for trial, while Gen. Pope ordered all detained be tried. 303 were given death sentences that were subject to Presidential review. Lincoln ordered Pope send all trial transcripts to Washington, where Lincoln and two of his staff examined them. Lincoln realized the trials could be divided into two groups: combat between combatants and combat against civilians. The groups could be identified by their transcripts, the first group all had three pages in length while the second group had more, some up to twelve pages. He placed 263 cases into the first group and commuted their sentences. In the second group were forty cases. One he commuted for becoming a state's witness. Sibley dismissed another when proof surfaced exonerating the defendant. The remaining 38 were executed in the largest mass hanging in U.S. history. Questions arose concerning three executions that have not been answered. Less than 4 months afterwards, Lincoln issued the Lieber Code, which governed wartime conduct of the Union Army, by defining command responsibility for war crimes and crimes against humanity. Congressman Alexander Ramsey told Lincoln in 1864, he would have gotten more re-election support in Minnesota had he executed all 303 of the Mdewakanton. Lincoln responded, "I could not afford to hang men for votes." The men whose sentences he commuted were sent to a military prison at Davenport, Iowa. Some he released due to the efforts of Bishop Henry Whipple.