Kelley joined the Guards Military Company of Wheeling and eventually became commander of the Fourth Virginia Regiment, a uniformed militia unit. When the war became imminent, Kelley had been working as freight agent for the Baltimore & Ohio Railroad in Philadelphia, he returned to Wheeling to be commissioned colonel of the first regiment to be recruited loyal to the Union on southern soil. On May 25, 1861 he was ordered by General George B. McClellan to assume command of all troops in Western Virginia and to advance on the Confederates on May 27th. The poorly equipped and poorly organized volunteers boarded a B&O train and headed for Grafton which was held by the Confederates under Colonel George A. Porterfield. The trip was delayed by burned bridges beginning at Mannington so that the unit did not reach Grafton until June Ist. The First West Virginia was joined by the 16th Ohio and the 9th Indiana regiments. The Confederates had left Grafton and headed toward Philippi. Kelley's force marched all night through a driving rain and attacked the Rebels at 4 a.m. on June 3rd, in what is considered to be the first land engagement of the Civil War.
     The battle really didn't amount to much. Kelley's units chased the Confederates out of Philippi and down the road toward Beverly. However, there was an exchange of gunfire and Kelley was wounded, the first Union officer to be wounded in battle. Struck in the right breast with the bullet lodging near his shoulder blade, it was thought to be fatal. He was appointed brigadier general with the appointment to date from May 17th which made him a ranking general in future years.
     Kelley served throughout the Civil War and had a checkered career most of which centered around the defense of the B&O railroad which was a vital supply link for the Union Army.
     Kelley is remembered most frequently for two events. The first was the so-called Battle of Philippi which I have briefly described. The other was his spectacular capture late at night from his hotel room in Cumberland, Maryland where he had his headquarters during most of the war, along with General George Crook and his Adjutant General, Major Thayer Melvin, on the night of February 21-22, 1865. More about this event later.
     For much of the Civil War, Kelley was responsible for the region from Cumberland, Maryland to the southernmost parts of what is now West Virginia. While he had a fairly large force at his disposal most of the time, the distances involved and the mountainous terrain made it a huge task. To be more succinct his responsibility was to maintain control of the Baltimore and Ohio Railroad and to keep the Confederates from moving west into the Western counties of Virginia, now West Virginia, and the Ohio Valley. The object was to maintain clear communications for men and supplies for the Union forces East of the Alleghany Mountains. He wasn't always successful in doing this but neither were Generals, Wallace, Shenck, Sigel, Hunter, and Crook. The Union never had undivided control of the West Virginia District until late in 1864 when General Philip Sheridan defeated the Confederates under General Early and General Lee's Army was bottled up during the seige at Petersburg.
     Never completely defeated or controlled were the partisan Confederate units that roamed the lower Shenandoah Valley, Western Maryland and the Potomac River basin. Most notably were the partisans under Colonel John Mosby and Captain John Hanson McNeill.