Sullivan helped recruit and organize a three-months'
infantry regiment, the
6th Indiana Volunteers. He was elected as a
captain and led his troops into combat at the
Battle of Philippi in
western Virginia. Following the expiration of his term of enlistment, Sullivan mustered out of the army. However, he soon received an appointment from
Governor Oliver P. Morton as the
colonel of the
13th Indiana, a three-years' regiment. Sullivan returned to western Virginia in the army of
George B. McClellan and fought at
Rich Mountain and
Cheat Mountain in the summer of 1861. In the spring of 1862, Sullivan commanded a
brigade of infantry during the
Valley campaign and led it into action at the
First Battle of Kernstown. He was commissioned as
brigadier general to date from April 28, 1862. Later in the spring, he was transferred to the
western theater and assigned command of a brigade in the
Army of the Mississippi, serving under
William S. Rosecrans. Sullivan again saw combat in the battles of
Iuka and
Corinth in
Mississippi. In the autumn of that same year, Sullivan was given command of the District of Jackson, Tennessee, and its widely scattered garrisons of Union troops. There, his men were often pitted against the raiders of
Confederate general
Nathan B. Forrest, including the
Battle of Parker's Crossroads, December 31, 1862.. Late December, Sullivan received General Grant's General Order #11, December 17, 1862, ordering the expulsion of all Jews in his military district. Sullivan refused to execute the order according to Rabbi Isaac Mayer. "He thought he was an officer of the army and not of a church." Four days later, Sullivan was forced to comply. Abraham Lincoln revoked Grant's General Order January 4, 1863. During the 1863
Vicksburg campaign, Sullivan served on the field staff of
Maj. Gen. Ulysses S. Grant as the acting
inspector general for his army. Following the surrender of Vickburg on July 4, Sullivan took the position of
Chief of Staff for Maj. Gen.
James B. McPherson. In September, he was reassigned to the Department of West Virginia to serve under his father-in-law, Maj. Gen.
Benjamin F. Kelley. Given command of a
division, Sullivan was tasked with protecting the vital
Baltimore and Ohio Railroad in
Western Maryland. In mid-October 1863, he led a column from
Harpers Ferry that thwarted an attack on
Charlestown, West Virginia, by Confederates under
John D. Imboden, driving the enemy up the valley. During the
Valley campaigns of 1864, Sullivan drew the ire of his superior,
David Hunter, for his lack of initiative and was replaced by Brig. Gen.
George Crook on July 16. Sullivan was never again given a significant command. He resigned from the army on May 11, 1865, and tellingly was not among the scores of Union generals who received
brevet promotions to higher rank at the close of hostilities. ==Postbellum career==