After receiving a colonel's commission from Governor Oliver P. Morton, Reynolds was placed in command of Indiana'sCamp Morton, the wartime state's militia muster encampment at Indianapolis. Reynolds's 10th Indiana Volunteer regiment was sent to western Virginia, where it played a decisive role repulsing Confederates under Robert E. Lee at Cheat Mountain. Although promoted to brigadier general, Reynolds resigned in January 1862 and resumed training Indiana regiments at Camp Morton until November 1862 without a commission. Retroactively appointed colonel of the 75th Indiana volunteers, brigadier general with orders to build a depot and field works in Carthage, Tennessee, and then major general of U.S. volunteers, Reynolds commanded a division of XIV Corps, Army of the Cumberland, at Hoover's Gap and Chickamauga. After serving as the army's chief of staff before Chattanooga, Reynolds was transferred to the Gulf of Mexico, where he led a division of XIX Corps that garrisoned New Orleans, Louisiana. He was later promoted to the command of the XIX Corps, and then commanded VII Corps in Arkansas. He was the brother-in law of Brevet Brigadier General Jules C. Webber.
Reynolds participated the Black Hills War, of 1876-1877, and led the Big Horn Expedition out of Fort Fetterman, Wyoming Territory, on March 1, 1876 in search of "hostile" Lakota Sioux and Northern Cheyenne Indians under Sitting Bull and Crazy Horse. On the morning of March 17, 1876, Reynolds and six companies, about 379 men of the 2nd and 3rd United States Cavalry Regiments attacked a Northern Cheyenne and Oglala Lakota Sioux village on the Powder River, in what became known as the Battle of Powder River. The Native Americans were camped on the west bank of the River in southeastern Montana Territory when Reynolds' soldiers attacked it, and after a five-hour-long engagement, suffering four men killed, six wounded, 66 frostbitten, and inflicting only a few killed and wounded, he withdrew his men from the battlefield and retreated about to the south. Native American leaders in the village at the time were Two Moon, He Dog, Little Wolf, and Wooden Leg. During the battle, He Dog rode a horse belonging to Crazy Horse, who was camped only about to the north during the battle on St. Patrick's Day. Reynolds's winter campaign of March 1876 ended in failure and he was subsequently court-martialed for three charges. He was found guilty of all of the charges and given the sentence of suspension of rank and pay for one year's period. Joseph Reynolds resigned from the United States Army on June 25, 1877.
Death
Joseph Jones Reynolds died on February 25, 1899, in Washington, D.C., at the age of 77, and is buried in Arlington National Cemetery.