In 1861, McClernand received a promotion to brigadier general. His promotion was a political move by Abraham Lincoln to hold the Southern Illinois Democrats. In March 1862, he rose to the rank of major general, participating in the Battle for Arkansas Post, for which he was rewarded with the command of the XIII Corps. At Vicksburg, under the eye of Ulysses S. Grant, he failed to demonstrate any skill as a field commander, so he was sent home by Grant. He returned to field in the next year in Louisiana and in Texas. However, he finally resigned from the army in November 1864.
