For the first three and a half years of the War between the States, the military actions took place simultaneously in two different areas: a small area in northern and northeastern Virginia and a western area in the region bounded by the Mississippi River, the Cumberland River, and the Appalachian Mountains. For most of the war, the Confederate forces were on the defensive side. With General Robert E. Lee as Commander-in-Chief, the Confederates had unity of command whereas the Union forces actually had five successive generals before appointing Ulysses S. Grant as the supreme commander. Many of the best military minds were fighting on the Confederate side, and it is believed by several historians that only their great strategic ability and planning against larger military forces with better equipment and clothing kept the war from being concluded at a much earlier date.
The major objective of the Federal government became a clearcut one, namely, to capture Richmond, the capital of the Confederacy. Thus, a chief aim of the military forces in Virginia was the protection and defense of Richmond at all times. Virginia lost Accomack and Northampton Counties on the Eastern Shore at the beginning of the war and was unable to obtain control of Union Fort Monroe.
On May 24, 1861 the Fire Zouaves, a unit of the United States Army, marched from Washington to Alexandria, the first point of invasion in Virginia in the War between the States. They took possession of Alexandria in the name of the United States and found no organized opposition because there were no Southern troops here. Virginia had not been ready for war and had made no preparations for war. The only standing army in the state at the time of her secession was a group of soldiers whose duty had been to guard public property in Richmond. Several volunteer companies had organized in various parts of the state for the first time after John Brown's Raid. One of the first immediate tasks to be done was the training of soldiers in Virginia and the acquiring of cannon and fire-arms. Consequently, it was not unusual for Alexandria not to have had an organized force by May 24, awaiting Federal invasion. As these Fire Zouaves entered Alexandria, they noticed a Confederate flag flying from the top of a small hotel called the Marshall House. Colonel Elmer Ellsworth, the Federal commander, decided to obtain this flag. He entered the hotel, ran up the stairs to the roof and grabbed it. He had started to descend the stairs with his trophy when, at the first landing, he met the hotel owner, James W. Jackson, who had been curious to know who had been rushing up the stairs and invading his hotel. When he saw the Confederate flag in the hands of the Federal officer, he shot him in the breast. Ellsworth died instantly and Jackson was immediately killed by bullets and bayonets used by Ellsworth's troops. This was the first blood shed in Virginia in the War between the States.
A skirmish took place at Fairfax Court House on June 1, 1861, which caused the death of Captain John Quincy Marr of the Warrenton Rifles. His death is considered the first Confederate battle death.
In the same month, the first land battle of the War between the States took place around and near the town of Philippi located in western Virginia (today, in West Virginia). On June 3, Union troops led by Colonel B. F. Kelly clashed with Confederate troops led by Colonel George A. Portfield. This fighting was not only a victory for the Union forces, but the retreat of the Confederates from the surprise Union attack on a dark, rainy night was exceedingly rapid. The Confederates fled more than thirty miles in one day to a town called Beverly, thereupon earning for their action the title, the "Philippi Races."
On July 21, along a creek called Bull Run, near Manassas, approximately twenty-five miles from Washington, some Union forces under the leadership of General Irvin McDowell met Confederate forces under the leadership of General Pierre G. T. Beauregard. Manassas was the site of a key railroad junction, an important line of supply and communication. Although the Union forces were at first successful, the firm stand taken by the Confederate forces on Matthews Hill and on Henry Hill led by General Thomas Jonathan Jackson and a counter-attack led by Confederate General Joseph E. Johnston's forces resulted in chaos in the Union army and a panicky retreat to Washington. This was a most unexpected defeat for the Union forces. "J. E. B." Stuart served under Joseph Johnston at this time and led a successful mounted charge against the Federal infantry. He also helped create disorder and panic in their lines. This first Battle of Bull Run or Battle of Manassas was the occasion for T. J. Jackson's famous nickname: "Stonewall." General Bernard E. Bee, a South Carolinian, headed some troops which had become panicky, and, as he saw T. J. Jackson's brigade in correct line formation, he is said to have made the following comment to his group: "Look! There is Jackson and his brigade standing like a stone wall. Rally behind the Virginians." From that time on, T. J. Jackson was called "Stonewall" Jackson. As the Union forces neared Manassas, Captain Alexander, a Confederate officer, spotted their coming from his lookout station. He relayed their approach by wigwagging signals with flags. This action is believed to be the origin of semaphoring. This battle caused the North to realize that the conquering of the South was not the easy task that it had predicted or had assumed. Their military slogan "On to Richmond" became a military challenge rather than an accepted conclusion.
President Lincoln had declared a blockade of the Southern ports as soon as the war had started. The Federal Navy Yard at Norfolk was captured by the Confederates without resistance. The United States ships were only twelve in number at the beginning of the war, but others were quickly constructed. The Confederates hoped to keep the James River open at all times. They needed ships badly, having had no navy to draw upon for ships. When the Federal employees had abandoned the Norfolk Navy Yard, they had sunk a wooden frigate called the "Merrimac." Governor Letcher of Virginia ordered that this ship be raised and be converted into an effective, usable frigate. Lieutenant John M. Brooke, John L. Porter, W. P. Williamson and others planned together for a converted ship. Finally, the hull of the old ship was covered with pine, oak and iron plates from the famous Tredegar Iron Works of Richmond. It was equipped with ten guns and an inexperienced crew under the ex-United States Naval Commander, Franklin Buchanan. This iron-clad vessel was renamed the "Virginia," and it traveled to Hampton Roads to attack the Federal fleet on March 8, 1862. When it first received gunfire from a Federal ship, the shots surprisingly glanced off its sides. The vessel moved very slowly. When at close range, it pierced the "Cumberland" with its iron ram causing it to sink. The next day, much to its surprise, it was matched by a Union ship, the "Monitor," designed by John Ericsson, which was ironclad, smaller, more agile and newly constructed throughout. The ships fired upon each other, but they could not inflict serious damage. The Battle of the "Monitor" and the "Virginia" (formerly "Merrimac") was a draw or indecisive from a victory point of view. However, it is important historically as the first battle of ironclad vessels in the United States. The "Virginia" was later blown up when the Confederates evacuated Norfolk.
On March 23 of the same year, "Stonewall" Jackson became the aggressor and attacked a Union force at Kernstown, near Winchester. However, when one of his brigade became short of ammunition, he had to retreat southward. This battle was the beginning of Jackson's "Valley Campaign."
Beginning on April 5 and continuing for approximately one month, an important siege took place at Yorktown. After a line of fortifications had been erected across the Peninsula from the Warwick River to Yorktown by the Confederate Commander John B. Magruder, General Joseph E. Johnston entrenched his army here. Union General George B. McClellan coming from Fort Monroe besieged the area for weeks and finally mounted his large size guns. With this action, Johnston withdrew since he was not equipped for such heavy fighting. As General Johnston's forces were retreating from Yorktown, they met an advance section of McClellan's army about one mile east of Williamsburg. Johnston was forced to fight at this time because he did not want them to capture his wagon train. Both armies fought valiantly, and neither side could get the advantage of the other. When night came, after a rainy day of fighting, Johnston retreated westward toward Richmond under cover of darkness. Two days later, Union General W. B. Franklin attempted to intercept Johnson on his retreat toward Richmond by landing just south of West Point on the eastern bank of the York River. However, General G. W. Smith came to Johnston's rescue and successfully drove Franklin forces back to the York River in order that Johnston could continue on his way to Richmond.
On May 8, 1862, "Stonewall" Jackson decided to prevent two Union generals, John C. Fremont and Nathaniel P. Banks, from combining their forces. He selected a position on a mountain top near McDowell, a village in Highland County. When Fremont's troops arrived under the leadership of General R. H. Milroy, they rushed up the sides of the mountain, only to be attacked by the Confederate forces under Jackson and driven back to a retreating position.