Shiloh. Upon arrival, the regiment led an attack that captured the Washington Artillery Battery of New Orleans. He was shot through the feet during a Confederate counter-attack, but continued until wounded again with a shot through the right jaw. He was thought to be mortally wounded, and Whitelaw Reid, then a correspondent for the Cincinnati Gazette, had seen Runkle's wounds and filed a glowing obituary saying in part "He died a hero. Green grow the grass above his grave." Runkle not only survived but outlived Reid, and in turn praised him in an obituary. He was promoted to lieutenant colonel in May 1862. 45th Ohio Infantry After recovering from his wounds, on August 19, 1862, he was commissioned Colonel of the 45th Ohio Infantry. The regiment was ordered to Cynthiana, Kentucky, where it remained until General Kirby Smith's advance following the Confederate victory at the Battle of Richmond, Kentucky on August 30, 1862, forced the 45th Ohio, along with the 99th Ohio Infantry, to pull back to the Ohio River at Covington, Kentucky, where they participated in the Defense of Cincinnati. In mid–February the regiment was mounted at Danville, Kentucky, and Colonel Runkle commanded the brigade formed by the mounted 45th Ohio along with the 7th Ohio Cavalry and 10th Kentucky Cavalry regiments. Runkle's men broke the enemy line at the Battle of Dutton's Hill in Somerset, Kentucky on March 30, 1863, and he was thanked for his gallantry on the field by Quincy Gillmore, the commanding general, who gave Colonel Runkle's command entire credit for the victory. Fought in the Battle at Monticello, Kentucky on May 1, 1863, where Confederate forces under General Pegram were driven from the field. Other commands From July 1863 to January 1864, while recovering from wounds, he served on the staff of Ohio governor David Tod and led Ohio Militia units in response to Morgan's Raid. He later commanded the 3rd Brigade of the 4th Division of the XXIII Corps in Kentucky and Tennessee and participated in Sherman's Atlanta Campaign at the battles of Rocky Face Ridge and Resaca. Runkle was honorably mustered out July 21, 1864, and on August 29, 1864, he was appointed lieutenant colonel in the Veteran Reserve Corps where he commanded the 21st Regiment until the war ended. Freedmen's Bureau While in the Veteran Reserve Corps, Runkle was assigned to work at the Bureau of Refugees, Freedmen, and Abandoned Lands