During the Peninsula campaign the fighting for Richmond began at Fair Oaks. General Johnston was wounded during his attack on Union forces and was replaced by General Robert E. Lee.
Confederate General Johnston was badly wounded at the Battle of Seven Pines. Aside from that, Lee was the better General. Johnston gave up ground when he did not have to, and he did not work and play well with others.
On May 21, 1862 Confederate President Jefferson Davis demanded the battle plans of Major General Joseph Johnston's defense of Richmond. Davis had realized that Johnston had no intentions of using the Peninsula as a base for his defensive operations against the Union forces on their way to assault Richmond. Finally, General Lee and Davis convinced Johnston to attack Union General McClellan's forces east of Richmond on the peninsula. Johnston's refusal, then reluctance to do so, would later become evident in the Atlanta campaign when Johnston would be replaced by John Bell Hood. Davis and Johnston would never get along with each other throughout the war.
General Sherman began his campaign into Georgia with 100,000 troops. His Confederate opponent, General Joseph Johnston commanded only 50,000 troops.
In the midst of the McClellan Peninsula campaign, Confederate General Joseph Johnston was wounded and was out of action. Jefferson Davis was aware of Robert E. Lee's talents, and had placed Lee in charge of defeating the Peninsula campaign. Lee was always a well respected Union commander. With his success in the Peninsula campaign, Lee took over Eastern Confederate military operations.
When General Lee was called to replace the wounded Joseph Johnston to stop the Union's Peninsula campaign, he left General Gustavus W. Smith to defend Richmond. Smith was ready having recovered from an illness in early June 1862.
During the Peninsula campaign headed by Union General George B. McClellan, he for some unknown reason decided to lay siege to Confederate troops in Yorktown. On May 3, 1862, commanding Confederate General Joseph Johnston decided to evacuate his troops at Yorktown.
Confederate General Joseph Eggleston Johnston.
When Confederate General Joseph Johnston refused to obey the orders of the Confederate Secretary of War, James Seddon, President Davis had every reason to relieve Johnston of duty. Despite the past disagreements with Johnston, and what would turn out to be future disagreements, President Davis did not fire Johnston. Instead, recognizing his good points, Davis tried to help him. He did so by exploring with him the possibility of a campaign into Kentucky.
Jefferson Davis believed that General Joseph Johnston was a superior general. He had defended Richmond in the Peninsula campaign and won the first Battle of Bull Run with PT Beauregard. Davis decided Johnston could handle an assignment in the West so in November of 1862, he sent Johnston to command the South's Western Department. This comprised Tennessee, Alabama, Mississippi and the eastern area of Louisiana.
Near the end of May, 1862, Confederate General Joseph A. Johnston decided to attack the advance units of Union General George B. McClellan in the Battle of Seven Pines. The assault was a failure and early on in the war, Johnston was made aware of the danger of assaulting enemy forces in rough terrain. Rebel losses, including the wounding of Johnston himself, required that Confederate Davis place Robert E. Lee in charge of combating McClellan on the Peninsula. Some historians claim that Johnston's lesson there prevented him to later have the ability to take risks. As an aside, Johnston was relieved by Davis in the Atlantic campaign because of his aversion to make assaults.
Joseph E. Johnston was a General in the Confederate States Army .
By late April of 1862, it became clear that the Union's supremacy in heavy artillery would force the Confederates to abandon Yorktown. The Confederate commander of Southern troops on the Peninsula at that time was Major General Joseph Johnston. At that time Johnston was pessimistic about the campaign and on May 1, 1862, ordered his generals to prepare for a retreat. The Union forces at that time numbered 100,000 and the Southern army had 70,000 troops.