Though offered a commission by Louisiana after President Abraham Lincoln's call for volunteer troops in April 1861, Daniel returned to Halifax and instead offered his services to his native state. He was chosen colonel of the 4th Regiment of infantry. When the period of enlistment expired, he was offered several positions, commanding the 43rd North Carolina Infantry or 45th North Carolina Infantry as well as the 2nd North Carolina Cavalry. He accepted the command of the 45th Regiment as its colonel. Daniel led four regiments from Raleigh to Goldsboro and organized them into a brigade; afterward, he organized two other brigades. In June 1862, he was ordered to Petersburg, Virginia, where his brigade joined General Robert E. Lee's Army of Northern Virginia just before the Seven Days Battles, though it took no active part in the combat. Daniel was commissioned brigadier general on September 1, 1862, making him one of five men from Halifax County to attain that rank in the Confederate Army. He spent the fall of 1862 with his brigade at Drewy's Bluff in Virginia and subsequently served in North Carolina, although his unit saw limited combat action. Shortly after the Battle of Chancellorsville, he was transferred to Maj. Gen. Robert E. Rodes's division of Richard S. Ewell's Second Corps, where he served with distinction in the Gettysburg Campaign. Daniel's large brigade, entrusted to bear the Corps Flag, consisted of the 32nd, 43rd, 45th and 53rd North Carolina, as well as the 2nd North Carolina Battalion. On July 1, 1863, Daniel's Brigade repeatedly attacked the Union positions on McPherson's Ridge, eventually driving off the Union brigade of Col. Roy Stone. Initially, after his brigade's first assault was repulsed, Daniel heroically galloped about his retreating men, successfully rallying them and launching another assault. Daniel's men suffered the greatest losses of any brigade in the corps on the first day of the battle. During the Battle of Spotsylvania Court House on May 12, 1864, Daniel led his brigade in a fierce counterattack on the "Mule Shoe", trying to recapture the important position from elements of the Army of the Potomac, which had captured it at dawn. He was struck in the abdomen by a Minié ball, inflicting a mortal wound. He died the next day in a field hospital. His body was taken to Halifax and buried in the old colonial cemetery. Unknown to Daniel, Robert E. Lee had recommended his promotion to major general just prior to his death. Fellow North Carolina general and close personal friend Bryan Grimes later wrote, "He was decidedly the best general officer from our state. Though in all probability I gained a brigadier at his death, I would for the sake of the country always remained in the status quo than the country should have lost his services." General Grimes named one of his sons Junius Daniel Grimes. The Junius Daniel Chapter of the United Daughters of the Confederacy of Weldon, North Carolina, was named in the general's memory and honor.
