On December 13, the Battle of Fredericksburg took place between Confederate forces under General Lee and Union forces under General Ambrose Burnside. Burnside had supplanted General McClellan. The town itself was used as a battlefield and many of the individual houses were completely destroyed. The city had been evacuated when it was first bombarded by Burnside on December 11. He proceeded to use five pontoon bridges to get his troops across the Rappahannock River. Although this battle resulted in some of the heaviest losses of the war, Burnside with his remaining forces was finally driven back across the Rappahannock River with the Union casualties twice as many as the Confederates.

On March 8, 1863, an unusual incident occurred. At midnight, a group of Confederate raiders, led by Colonel John S. Mosby, made a raid on the Fairfax Court House which had become federally occupied. Noted for its ruthless guerilla actions, this group of raiders then made a daring invasion of the Union lines and continued to the headquarters of Union Brigadier-General Edwin H. Stoughton. After cleverly getting past Stoughton's guards in the middle of the night, Mosby himself quickly captured Stoughton as a choice Confederate prisoner.

On April 30, 1863, the Union army under General Joseph E. Hooker, Burnside's successor, crossed the Rappahannock River again, this time at Chancellorsville, approximately ten miles north of Fredericksburg. "Stonewall" Jackson was in charge of the attack on Hooker at Chancellorsville and his troops were forcing back the troops under Hooker when fate seemed to take a hand. On May 2, "Stonewall" Jackson had ridden beyond his own line of battle and was returning at dusk when he was mistaken for one of the enemy and was fired upon by a group of his own soldiers. He was wounded in the left shoulder, forearm and right hand and had to have his left arm amputated the next day. He was mortally wounded and died on May 10. His death was a great shock to the Confederate forces. General A. P. Hill had also been wounded at Chancellorsville. "J.E.B." Stuart voluntarily took command of the corps originally under Jackson and by his own audacious actions successfully led them in pursuit of the Union forces under Hooker, as Jackson had originally planned. Attacked by troops from the west under Stuart and by forces from the east under Lee, Hooker and his army were finally driven back across the Rappahannock River.

On June 9, the famous Confederate cavalry leader, "J.E.B." Stuart, met in combat the great Union cavalry leader, General Alfred Pleasanton at Brandy Station, near Culpeper. Stuart had been on a scouting trip between the Union forces and Washington, seeking information for the proposed advance of Lee to Gettysburg; Pleasanton had been seeking Confederate information for General George G. Meade, who had succeeded Hooker in command of the Union Army. Both cavalry groups consisted of approximately 10,000 troops each. Excellent horsemanship was displayed in this action with sabers as the chief weapons. Pleasanton and his men inflicted much damage and then left in orderly fashion. Stuart withstood the surprise attack very well and did not retreat in a panic, as might have been expected. Since the Unionists lost more men than did the Confederates in this practically evenly-matched fighting, the Battle of Brandy Station is considered as a notable victory for "J.E.B." Stuart and his men because Pleasanton had a highly skilled group of infantrymen. This battle was the first real cavalry battle of the War between the States. It is considered by many military strategists as the greatest cavalry battle of the nineteenth century. As soon as his battle ended, Stuart made another famous ride directly behind the Federal fighting lines. He was later criticized for this trip, however, because he had not been ordered to make such a trip and was badly needed by Lee at this time to screen planned operations and to keep Lee informed of the activities of Meade and his troops.

From June 13 to June 15, 1863, a second Battle of Winchester occurred. Union General R. H. Milroy was forced to evacuate Winchester and retreat across the Potomac due to the hard fighting of Confederate General Richard S. Ewell whose troops had captured not only valuable cannon and wagons but also approximately 4,000 Union soldiers.

At the beginning of the War between the States, forty western counties of Virginia preferred not to secede from the Union. Consequently, when Virginia joined the Confederacy, a majority of the residents of the western counties voted to secede from Confederate Virginia at a special Wheeling convention. They formed a separate Unionist Virginia government and selected Francis H. Pierpont as their Governor. They had already chosen two United States Representatives from their Virginia government and they proceeded to elect two United States Senators. State officers of the Unionist Virginia government were required to take an oath of allegiance to the federal government. This Pierpont government was accepted by the President of the United States and Congress as the official government of Virginia. Three months later, at a second Wheeling convention, the strong desire on the part of many residents of this area to become a separate state in the Union resulted in Pierpont's calling together his legislature which gave the necessary consent for the creation of an independent state from within the original state of Virginia government boundaries. The new area was first called "Kanawha" but later the name was changed to West Virginia. On June 20, 1863, West Virginia was admitted as the thirty-fifth state to the Union. Although this procedure was apparently illegal and unconstitutional because the United States Constitution provides that no new state can be formed within the jurisdiction of any other state without the consent of the state legislature so involved, President Lincoln and the United States Congress overlooked this technicality because of a need for military and political expediency in wartime. Governor Pierpont and his Unionist government in August 1863 changed the location of his "restored" or "reorganized" government from Wheeling to Alexandria, which he termed the West Virginia capital city at that time. Alexandria maintained this West Virginia capital city status until the end of the war and the residents of Alexandria were forced to live under the provisions of a Pierpont-drafted "state" constitution. Later, Berkeley County and Jefferson County were annexed to West Virginia by November 1863 and became an official part of the state of West Virginia. Eventually, Virginia lost fifty counties altogether to West Virginia, approximately one-third of its total land area, with their human and natural resources as well as their financial support.

After the victories of Fredericksburg and Chancellorsville, Lee decided to cross the Potomac again and invade the north once more. When Lee found out that a large Union force under the command of General George G. Meade, who had replaced General Joseph Hooker, was at Frederick, Maryland, Lee decided to center his forces at Gettysburg, Pennsylvania. On July 1, 1863, the Confederate forces attacked Meade's forces and made temporary gains. Two days later, three Confederate brigades commanded by General George E. Pickett advanced to the Federal cannon center, now called Cemetery Ridge, where mass slaughter of the Confederates took place. On July 4, the remaining Confederates returned sadly across the Potomac River into Virginia. Approximately two weeks after the Gettysburg defeat, a surprise attack on Wytheville, Virginia, was thwarted by the courageous efforts of Molly Tyres who rode rapidly over forty miles of mountain road between Tazewell and Wytheville to warn the inhabitants of the coming attack. Thus, did Virginians—military and civilian—strive to help the Confederate cause in which they so strongly believed.

On May 5 and 6, 1864 the so-called Battle of the Wilderness was fought in the heavily forested terrain of Spotsylvania County. As General R. S. Ewell was returning his forces from Fredericksburg to Orange, he encountered General Ulysses S. Grant who had become commander of the Union army. At the same time forces under General Ambrose P. Hill encountered the left wing force under Grant which resulted in terrific fighting within the dense woods of the wilderness. As the left wing force under Grant was breaking through the forces under Hill, General James Longstreet approached and forced the Union troops back to Spotsylvania Courthouse, southwest of Fredericksburg. Grant retreated in this direction in an attempt to keep Lee away from Richmond. However, Lee was ahead of Grant. Although Grant tried repeatedly from May 8 to May 18 to break through the Confederate lines at Spotsylvania with exceptionally heavy musketry fire causing thousands of casualties, he was unable to penetrate Lee's lines. Therefore, he moved southward to the North Anna River.

In the meantime, on May 10, when General Philip Sheridan tried to make an unexpected rush on Richmond, "J.E.B." Stuart, with only part of his cavalry, blocked Sheridan's way at Yellow Tavern and saved the Confederate capital. Stuart was mortally wounded by a close pistol shot in this fighting and he died on May 11, 1864 in Richmond. He is considered by many military strategists as the greatest cavalryman in United States history.

On May 15, General Franz Sigel, a Union leader, decided to capture Staunton in order to ruin the communication system there which Lee had used to be kept informed about activities in the Shenandoah Valley. He arrived as far as New Market, in Shenandoah County, when he met Confederate General John C. Breckinridge who had a comparatively small army consisting mostly of young Virginia Military Institute cadets. They showed the benefits of their military training and successfully captured a Union battery. After this had been done, General Breckinridge advanced, defeated Sigel and drove him down the Shenandoah Valley.