McClellan was not present for the initial exchanges of the battle, having boarded the ironclad USS Galena and sailed down the James River to inspect Harrison's Landing, where he intended to locate the base for his army.

His 121,500-man Army of the Potomac, along with 14,592 animals, 1,224 wagons and ambulances, and 44 artillery batteries, would load onto 389 vessels and sail to the tip of the peninsula at Fort Monroe, then move inland and capture the capital, some 80 miles away.

[5] The lack of decisive action on the Virginia Peninsula spurred President Abraham Lincoln to order McClellan's army to move into positions close to Richmond.

On June 1, after an unsuccessful attack on Union forces, Jefferson Davis, the President of the Confederacy, appointed Robert E. Lee, his own military adviser, to replace Smith as the commander-in-chief of the Confederate armies.

After this series of conflicts that inflicted thousands of casualties on both armies, McClellan began to assemble his forces in an imposing natural position atop Malvern Hill.

[10] Malvern Hill, a plateau-like elevation in Henrico County, Virginia, provided an impressive natural military position about two miles (3.2 km) north of the James River.

"[16] A few days prior to the action on Malvern Hill, McClellan incorrectly believed the Army of the Potomac was vastly outnumbered by its Confederate foe,[17] and his fear of being cut off from his supply depot left him cautious and wary.

[18] On the night of June 28, McClellan told his generals he intended to move his army to a position on the north bank of the James River called Harrison's Landing, where they would be protected by Union gunboats.

[20] On the morning of June 30, 1862, the Union V Corps under Fitz John Porter, a part of McClellan's Army of the Potomac, amassed atop Malvern Hill.

This left 17,800 soldiers from Couch's and Morell's divisions at the northern face of the hill, overlooking the Quaker Road, from which the Federals expected Lee's forces to attack.

[22] Early the next day, Tuesday, July 1, McClellan, having come from nearby Haxall's Landing the night before, examined his army's battle line on Malvern Hill.

[25] Nonetheless, he left his troops at Malvern Hill and traveled downstream aboard the ironclad USS Galena to inspect his army's future resting place at Harrison's Landing.

Several pieces of evidence—abandoned commissary stores, wagons and arms, and the hundreds of Union stragglers and deserters his units had happened upon and captured—led Lee to conclude that the Army of the Potomac was demoralized and retreating.

"[29] Lee chose the relatively well-rested commands of D. H. Hill, Stonewall Jackson and John Magruder to lead the Confederate offensive, as they had barely participated in the fighting of the day before.

Hill's divisions were held in reserve as they were in no condition to fight after Glendale, with almost half their officers and close to a quarter of the enlisted men killed or wounded.

[28] As noon drew near with no sight of either Huger or Magruder, who were supposed to be manning the Confederate right flank, Lee replaced these two forces with the smaller units of Brig.

After a reconnoitering expedition on the right flank, James Longstreet returned to Lee; the two compared their results and concluded that two grand battery-like positions would be established at the left and right sides of Malvern Hill.

[39][c] On the Confederate right flank a total of six batteries[d] engaged the Federals, but they did so one-by-one instead of in unison, and each was consecutively cut to pieces by concentrated Union artillery fire.

[50] Not long after the advance of Armistead's regiments, John Magruder and his men arrived near the battlefield, albeit quite late because of the confusion regarding the names of local roads—by this time, it was 4 pm.

[54] The artillery of the Confederate left flank, under Jackson's personal command, also renewed their barrage with the late arrival of two batteries of Richard Ewell's division.

[59] The explosions and impacts of the gunboat fire impressed the Confederate troops, but the guns' aim was unreliable, and the large shells did considerably less damage than might have been expected.

[70] Ransom's men managed to come closer to the Union line than any Confederates that day, guided by the flashing light of the cannons amidst an encroaching darkness; however, George Sykes's artillery repelled that attack.

Gen. Porter summed up the Confederate infantry charges at Malvern Hill this way: As if moved by a reckless disregard of life equal to that displayed at Gaines' Mill, with a determination to capture our army, or destroy it by driving us into the river, brigade after brigade rushed at our batteries, but the artillery of both Morell and Couch mowed them down with shrapnel, grape, and canister, while our infantry, withholding their fire until the enemy were in short range, scattered the remnants of their columns, sometimes following them up and capturing prisoners and colors.

[91] Several other factors may have played into the Confederate repulse, including Theophilus Holmes's refusal to participate in the battle, dismissing any notion of actively engaging the enemy.

[45] Despite the strength of Malvern Hill, as demonstrated in the battle, McClellan felt he needed to continue with his planned withdrawal to Harrison's Landing, to Fitz John Porter's chagrin.

McClellan however insisted that Confederate troops greatly outnumbered his own, felt he could not protect Harrison's Landing from his current position at Malvern Hill, and feared being cut off from his supply depot.

[98] Lee ordered Theophilus Holmes to move to Drewry's Bluff, and decided to keep the men on Malvern Hill through July 3 to forestall any potential Union attack against that location.

[100] Despite the defeat on Malvern Hill, the Seven Days Battles accomplished the original Confederate goal of removing any direct threat to Richmond from the Union Army.

"[102] Similarly, Confederate Navy Secretary Stephen Mallory said, "the Great McClelland [sic] the young Napoleon now like a whipped cur lies on the banks of the James River crouched under his Gun Boats."

Several commanders were reassigned, including Theophilus Holmes and John Magruder,[105] and his army was reorganized into two wings, one under Stonewall Jackson and another under James Longstreet.