After the bloodbath at Gaines's Mill on June 27 and the small fights at Garnett's and Golding's farms on June 27 and 28, George McClellan had decided his army was lost. He ordered a full withdrawal from the Chickahominy toward Harrison's Landing on the James. The bulk of his army concentrated around Savage's Station on the Richmond and York River Railroad, preparing to push south through the difficult ground of White Oak Swamp. They did so without a leader. McClellan himself had ridden south of Malvern Hill after Gaines's Mill without leaving orders for the corps movements or naming anyone to command the retreat. The three corps left at Savage's Station, the II under Edwin V. Sumner, the III under Samuel P. Heintzelman, and one division of the VI under William B. Franklin, were on their own. McClellan considered Sumner, his senior, incompetent. So he simply appointed no one.

Robert E. Lee had crafted a converging plan to destroy the Army of the Potomac in mid-retreat. Longstreet and A.P. Hill would loop south through Richmond and strike at Glendale. Theophilus Holmes would push toward Malvern Hill. Stonewall Jackson, with his own division and those of D.H. Hill and William H.C. Whiting, would rebuild a bridge over the Chickahominy and drive south to link up with John B. Magruder, attacking the Federal rear guard at Savage's Station from the front. It was an ambitious plan, and almost none of it worked. Jackson, exhausted from his Shenandoah Valley campaign and inexplicably sluggish through the entire Seven Days, dawdled rebuilding bridges and then received a garbled order from Lee's chief of staff that convinced him to stay north of the river. He never came. Magruder was on his own, and so was the Union rear guard he was supposed to crush.

First contact came at 9 a.m. on June 29 in Mr. Allen's orchards two miles west of the station. Two Georgia regiments from George T. Anderson's brigade tangled with two Pennsylvania regiments for two hours; the Confederates lost 28 men and Brigadier General Richard Griffith, killed by a Union shell fragment. Magruder, reportedly dosed with morphine for a bout of indigestion, became convinced he was outnumbered and asked Lee for reinforcements. Two of Benjamin Huger's brigades came, then went back unused. By 5 p.m. Magruder had hesitated himself into attacking with only two and a half brigades, fewer than 14,000 men, against Sumner's 26,600. Heintzelman, meanwhile, had decided on his own that he was not needed and marched off without telling anyone, which is how Franklin and John Sedgwick discovered Kershaw's Confederate brigade approaching by mistakenly assuming the men in front of them were Heintzelman's. Magruder's attack came in with a strange new weapon: the Land Merrimack, a 32-pounder Brooke naval rifle on a railroad car, shielded by sloping iron casemate, pushed forward by a locomotive at marching speed. It was the first armored railroad battery ever used in combat. Its shells reached as far as the field hospital. The Vermont Brigade under William T.H. Brooks held the flank south of the Williamsburg Road; the Vermonters charged into the woods and were cut to pieces. The brigade lost 439 men. The 5th Vermont, under Lewis A. Grant, lost 209 of 428.

Darkness and thunderstorms ended the fighting in a bloody stalemate, about 1,500 casualties on both sides. Then, in the rain that night, the Army of the Potomac packed up and pulled out for White Oak Swamp. The twenty-five hundred previously wounded men in the field hospital were left where they lay. Jackson eventually crossed the Chickahominy at 2:30 a.m. on June 30, far too late to matter. Most of the Union army made it across White Oak Swamp Creek unmolested by noon. Lee reprimanded Magruder in writing: "I regret much that you have made so little progress today in the pursuit of the enemy." The fault, however, was wider than Magruder. It belonged equally to Lee's staff work and to Jackson's mysterious lethargy. The Seven Days would continue at Glendale and White Oak Swamp the next day, and the larger Battle of Malvern Hill on July 1, but the chance to destroy McClellan's army had passed in the orchards and woods west of Savage's Station.