Warner's arm had been shattered by the bullet and had to be amputated. He spent most of the rest of 1864 recuperating. He nominally became the commander of the 36th Wisconsin on October 27, when Colonel Brown resigned his commission due to his injuries, but Captain Cannon and then Captain George A. Fisk remained in operational command of the regiment until Warner was able to return to duty in December. The regiment remained camped near Petersburg until February 5, when they marched with II Corps to the vicinity of Hatcher's Run; they received shelling but were not actively engaged in the Battle of Hatcher's Run. They remained camped at Hatcher's Run until March 25, and during this time Warner received his official promotion to colonel.