Ellis volunteered for duty and was mustered in the 15th Regiment, 2nd Brigade, 4th Division of the Army of the Tennessee, in Freeport, Illinois. The 15th Regiment saw action at Fort Donelson near Clarksville, Tennessee, before action during the Battle of Shiloh. On April 6, 1862, while in the Hornet's Nest, having been promoted to the rank of acting colonel, Ellis was struck multiple times by enemy fire, but he continued to direct his troops until a fatal bullet hit him. After the battle, his body was recovered from the battlefield and his remains were shipped to Rockford for burial. After an elaborate funeral service, Ellis was buried in the family plot that he had bought only a few years earlier after the death of one of his daughters.