With the Army of the Potomac in full retreat, Robert E. Lee intended to cut the Federal host in two by thrusting the largest portion of his army—six divisions totaling 44,800 men—against the Yankees then gathered near Glendale. At the same time, Stonewall Jackson's four divisions were to engage the Union rearguard at White Oak Swamp. In order to ensure the success of his scheme, Lee planned to employ every unit in his army except the division of Theophilus Holmes and J.E.B. Stuart's cavalry.

George B. McClellan would not be sharing in his army's struggles this day. On the morning of June 30, the Young Napoleon boarded the Union gunboat Galena and spent the rest of the day completely cutoff from all communications with his beleaguered army. He left behind a leaderless force that occupied a patchwork defensive position stretching from White Oak Swamp to Malvern Hill on the James River. Without McClellan there to direct them, each corps and division commander posted his troops and fought the battle, in the words of one corps commander, "according to his own ideas."

In what was becoming a sadly recurring theme of the campaign, poor communication, confusion, and lackluster performances among the Confederate generals once again threatened to sap Lee's attack of all its energy. Two divisions of Union infantry and six batteries under the temporary command of William Franklin guarded the army's northern flank along White Oak Swamp, preventing a sluggish and cautious Stonewall Jackson from materially contributing to the day's action. At the same time, Benjamin Huger's Confederate division wasted hours cutting a new road through the thick woods and never participated in the battle.

Shortly after 4:00pm an impatient Lee ordered James Longstreet's and A. P. Hill's divisions forward in the direction of Willis Church. The Southerners routed George McCall's Pennsylvania Reserve division and captured McCall. Disparate Union counterattacks resulted in fierce hand-to-hand fighting but somehow managed to seal the breach. When the sun set over Glendale, the Yankees still held their line of retreat along the Willis Church Road. In the darkness, the Army of the Potomac made its way to Malvern Hill. Lee had lost his best chance to end the Union army's retreat.