When hostilities broke out between the
North and
South, Comly enlisted in the
Union Army in December 1861, being appointed by Republican Governor
William Dennison as
major of the
23rd Ohio Volunteer Infantry, an appointment at first not popular with the men as several experienced
captains were passed over for the political appointee, Comly. The regiment was assigned to
Raleigh, North Carolina, and Comly participated in several battles in the state. He was promoted to
lieutenant colonel. When the commander of the regiment, Rutherford B. Hayes, was wounded at the
Battle of South Mountain, Comly assumed command and led the 23rd OVI at
Antietam and several subsequent campaigns in the
IX Corps until Hayes recovered. In 1863, Comly married Elizabeth Smith, the daughter of the
Surgeon General of Ohio. In February 1864, when Hayes was promoted to division command, Comly was named as his successor as
colonel of the regiment, which he led for much of the remainder of the war until lingering effects from battlefield wounds forced him out of the field in early 1865. On January 13, 1866,
President Andrew Johnson nominated Comly for appointment to the grade of
brevet brigadier general of volunteers, to rank from March 13, 1865, and the
United States Senate confirmed the appointment on March 12, 1866. ==Postbellum==