Front lines
Immediately following the outbreak of the American Civil War in 1861, Hovey was commissioned as a colonel and organized the First Regiment of the Indiana Legion, a militia force that was used to defend the state during the war. Shortly thereafter, he was appointed colonel of the 24th Regiment Indiana Infantry. His regiment was quickly sent to the front-lines where he led it in the Battle of Shiloh in 1862. He remained with the advance elements of the main western Union army, and was promoted to brigadier general of United States Volunteers. During the siege of Corinth he commanded the 1st Brigade in Lew Wallace's 3rd Division. Hovey briefly commanded the District of Eastern Arkansas during the Fall of 1862 but returned to brigade command in the Army of the Tennessee in 1863.
On December 17, 1862, General Ulysses S. Grant issued his infamous, rabidly antisemitic General Order #11, expelling all Jews as a class from his military district (parts of Tennessee, Mississippi, & Kentucky). General Hovey was one of General Grant's most fervent supporters of Grant's Jewish Expulsion Order.
President Abraham Lincoln, upon learning of General Grant's order expelling all Jews, immediately rescinded it.
In January Hovey was given command of the 12th Division in the XIII Corps. He led his division at the Battle of Champion Hill later that year earning the praise of General Ulysses S. Grant.
He again led his division in the Siege of Vicksburg, breaking Confederate control of the Mississippi River. Grant again praised Hovey as key to the siege's success. Shortly after the battle, he received word that his wife had died, and returned home to arrange for guardians for his children. Her death was deeply saddening to Hovey who was slow to recover emotionally. He returned briefly to the front in 1864 to the 1st Division in the XXIII Corps division during the Atlanta campaign. In August 1864 the 1st Division was discontinued and its regiments dispersed throughout the other divisions in the XXIII Corps. Hovey, without a command, again returned home. For the remainder of the war he was in command of the military District of Indiana. He resigned from the Union Army on October 7, 1865.
