General Joseph E. Johnston, who had hastened to the Peninsula after the evacuation of Manassas, was now in chief command in front of McClellan. Leaving a strong guard at Williamsburg to check the pursuers, Johnston fell back with his main army toward Richmond, with the intention of fighting the Nationals when they should approach that city. But he was compelled to fight sooner than he expected, for gallant and energetic men-Generals Hooker, Kearney and Hancock-attacked that rear-guard on the 5th of May. Hard pressed, Johnston sent back a large portion of his army to help them. A sanguinary battle followed. Hooker began the assault, knowing a large body of troops were within supporting distance, and for full nine hours he bore the brunt of the battle. Then Kearney came to his aid, and, Hancock having turned the flank of the Confederates, the latter precipitately retreated. In this perilous movement they were led by General James Longstreet, the ablest and best of the Confederate leaders in the war.

On the morning after the conflict, McClellan came upon the battle-field, just as the victors were about to press on in pursuit of the fugitives, who had left about eight hundred of their wounded behind them in their flight. He had kept Franklin so long at Yorktown, that the latter could not flank the Confederates; and now, when the latter were flying evidently in a panic, the Commander-in-Chief would not allow a pursuit, but moved leisurely forward during the next ten or twelve days, reaching the Chickahominy River when Johnston was safely encamped beyond it. Experts on both sides declared, that had a vigorous pursuit followed the events at Williamsburg, the Confederate army might have been captured or dispersed. Franklin had secured a firm foothold at near the head of the York River, which was made the base of supplies for the Army of the Potomac in its earlier operations against Richmond. In the battle at Williamsburg, the Nationals lost twenty-two hundred men, of whom four hundred and fifty-six were killed. The Confederate loss was about one thousand.

More than a month, after General McClellan arrived at Fortress Monroe, had been consumed in moving only thirty-six miles toward Richmond, and the army had suffered fearful losses by sickness. Very few perished by the weapons of the enemy during the month's siege of Yorktown, "but disease," said General J. G. Barnard, McClellan's chief engineer, in his report at the close of the campaign, "took a fearful hold of the army; and toil and hardships, unredeemed by the excitement of combat, impaired their morale. We did not carry with us from Yorktown so good an army as we took there. Of the bitter fruits of that month gained by the enemy, we have tasted to our heart's content." Twenty of the thirty days that the army lay before Yorktown were marked by heavy thunder-showers, following in quick succession. The troops, wearied and overheated by labor, lay on the damp ground at night, and were chilled. "In a short time," wrote Dr. Marks, a participant, "the sick in our hospitals were numbered by thousands, and many died so suddenly that the disease had all the aspects of a plague."

One cause of McClellan's tardy advance was his constant fear of not having troops enough to meet the energetic Johnston. Before his army left Washington, Blenker's division of ten thousand men were taken from it to strengthen Fremont, who was in command of the Mountain Department beyond the Blue Ridge; and soon afterward McDowell's army corps were detached from McClellan's immediate command, and its leader instructed to report directly to the Secretary of War.