With the approval of the plans for the campaign, the Army of the Potomac began sailing from Alexandria to Fort Monroe on March 17. This marked the beginning of the Peninsula Campaign in which perhaps as many as 155,000 Federals and 95,500 Confederates eventually became involved, although not that many were present at any one time.
McClellan began advancing from Fort Monroe early in April, but stopped for a month to besiege a much inferior Confederate force under Maj. Gen. John B. Magruder at Yorktown. During the siege, Johnston had time to join Magruder with his entire force. McClellan planned a major assault on May 5, but on May 3, Johnston began withdrawing up the peninsula. McClellan pursued, and the Confederate rear guard under Maj. Gen. James Longstreet fought a successful delaying action at Williamsburg on May 5 which developed into a major engagement, resulting in 1,866 Union and 1,570 Confederate casualties. McClellan continued his pursuit in leisurely fashion, established his main base at White House, and toward the end of the month pushed 2 corps southwest across the Chickahominy River toward Richmond. His remaining 3 corps stayed north of the river. McClellan expected help from the force under McDowell which had moved to Fredericksburg, but Jackson's Shenandoah Valley Campaign drained away half of McDowell's troops, and McClellan received only 2 divisions of reinforcements from this source during the campaign.
A heavy rain on May 30 flooded the Chickahominy, washing out bridges and rendering the stream unfordable. Recognizing this as an opportunity to defeat the Union force in detail, Johnston attacked the isolated Federals south of the stream near Fair Oaks on 31 May 31. The Federals, after suffering initial reverses, were finally able to repel the attack. Each side committed some 41,000 men during the 2-day engagement, the Federals losing 790 killed and 4,384 wounded, the Confederates 980 killed and 5,729 wounded.
Johnston was wounded at Fair Oaks and was replaced by Gen. Robert E. Lee. Jackson now moved quickly and with complete secrecy to Richmond, while Lee pulled back closer to Richmond and built fortifications. Late in June Lee struck hard on McClellan's right (north) flank and succeeded in cutting the Federal line of communications to the main base at White House. On July 2nd, in a heavy rainstorm, the Army of the Potomac abandoned its battlefield position on Malvern Hill, continuing its retreat across the Virginia peninsula. For a week, the federals, constantly withdrawing, had battled the Army of Northern Virginia. The Seven Days Campaign had been a series of running battles as maj. Gen. George B. McClellan shifted his supply base from White House on the Pamunkey River to Harrison's Landing on the James River. He termed it a strategic withdrawal, though some critics labeled it a "great skedaddle".
Harrison's Landing was a wharf on the 3-mile riverfront of the Berkeley plantation, the former manor home of the Harrisdon family and the birthplace of William Henry Harrison, the nation's 9th president. McClellan had selected the site because there was not any closer place to Richmond where the Union army could be supplied by water and protected by naval gunboats.
The Federals' arrival at the landing on the 2nd signaled the end of the 2-month Peninsular Campaign. After the past week's vicious battles, neither the Union troops nor the Confederates were capable of renewing combat. Gen. Robert E. Lee's Confederates pursued to Harrison's landing, but McClellan's lines, anchored between 2 creeks and supported by the gunboats' heavy ordnance, were too strong. Both armies needed a respite and only sporadic skirmishing characterized the action at the landing.
Pres. Lincoln visited McClellan on the 8th. Unwilling to admit his faults or accept blame, the army commander gave Lincoln his Harrison's Landing Letter. In it, McClellan boldly advised Lincoln on political and military policy.
The Union army remained at Harrison's Landing until ordered north on August 3rd. As usual, McClellan moved tardily, with the final contingent not leaving until after the 20th.
It was a hard fought, complex operation known as the Seven Days' Battles and included major engagements in Mechanicsville, Gaines' Mill/ First Cold Harbor, Savage Station, Frayser's Farm/ Glendale, and Malvern Hill. On July 3, Lee broke contact and returned his troops to the lines at Richmond. There was not anymore more fighting. Casualties had been heavy on the peninsula. Union losses in killed, wounded, and missing totaled 15,849; Confederate losses were 20,614.
In June 1862, during the Peninsula Campaign, Lincoln consolidated the Union forces in the Shenandoah Valley and other parts of western Virginia—some 45,000 men—as the Army of Virginia, assigning the commend to Pope. After Jackson moved to Richmond, Pope was given the mission of marching down the Shenandoah Valley and then east against Richmond to relieve McClellan. On 11 July 11, Lincoln appointed Halleck as General in Chief. By that time Pope's army was in western Virginia, and McClellan's Army of the Potomac, 100,000 strong, was at Harrison's Landing, with Lee in between.
Neither Halleck nor Lincoln liked the disposition of the forces, and on August 3, McClellan was ordered to Join Pope by way of Aquia Creek on the Potomac, a move that got under way about 2 seeks later.