Thereafter, Colonel Crooks served as colonel in the 6th Minnesota Volunteer Infantry Regiment and led five companies that fought against the Indians in the U.S.-Dakota War. Formed in Hokah, MN, the 6th Regiment was organized throughout the summer and fall of 1862 in response to President Abraham Lincoln's calls for a total of 600,000 additional troops. Over the course of the next two years, the regiment stayed in Minnesota due to the outbreak of the 1862 Dakota War despite the original plan to head south. Colonel Crooks was also president of a court-martial by which 100 Native American were condemned to death. His task was to bring about a revision of the findings of the bodies so that not more than 40 of the convicted Indians were executed. By the spring of 1864, the members of the Sixth Regiment were directed to carry on to Helena, Arkansas, on the Mississippi River. The Sixth Regiment, 950 total, arrived in Helena on June 23, 1864, and spent the next four months in unpredictable conditions. By this time, 58 enlisted men had died from malaria and over 650 people reported as sick. Finally in November, Colonel Crooks' troops were sent to fight under command of General E.R.S. Canby's campaign in Mobile, Alabama, and were in reserve during the April 9 capture of Fort Blakely. On August 19, 1865, William Crooks and his regiment returned home at last to Fort Snelling after a successful battle with the South.