atkins re-entered military service that fall when he was appointed the colonel of the 92nd illinois mounted infantry on september 4, 1862. by february 1863 he was given brigade command in the army of kentucky (department of the cumberland) until june 8. next he commanded a brigade in the army of the cumberland's reserve corps until july 15, when he was transferred to the department's cavalry corps. he then commanded two brigades of cavalry of the department of the cumberland and one in the military department of the mississippi in 1864 and into 1865. during these commands, he led a brigade of cavalry during major general william t. sherman's march to the sea.