Union General-in-chief Henry Wager Halleck expressed great concerns about the Middle Department's defensive strategy for its primary objective of protecting the Baltimore and Ohio Railroad corridor.

Ewell's movements were coordinated as part of an overall orchestration of the Army of Northern Virginia into position for crossing the Potomac River toward Pennsylvania by using the Blue Ridge Mountains as a screen.

This strategic offensive maneuver was put into effect on 3 June, when Gen. Robert E. Lee stated his intent to "transfer the scene of hostilities beyond the Potomac", by moving in a concealed fashion down the Shenandoah Valley.

[8] In response, Milroy posted McReynolds' brigade in Berryville, with orders to evacuate to Winchester upon the signal of the firing of one of the heavy artillery guns.

[10] Milroy also often recorded many other grand-sounding cavalry incursions supposedly capturing or killing many of Colonel John S. Mosby's rangers in the weeks and months leading up to June; however, the records of Mosby's Rangers do not corroborate or mention most of these engagements[11] Milroy's farthest outlying videttes to the south were located at or near Parkins Mill Battery at the Opequon Creek crossing, a mere 4 miles (6 km) south of Winchester.

The larger forts were named: The lesser fortifications initially used, but abandoned by Milroy during the course of the battle were: For further information see:The Occupation of Major General Robert Milroy Ewell and his generals were well acquainted with the tactical situation in Winchester, having fought through here under Lt. Gen. Jackson during the First Battle of Winchester, and understood the layout of the various fortifications and terrain masking opportunities on the west side of town.

Therefore, Ewell further split his main attack force of two divisions into two basic flanking movements: Johnson's division, while moving northwest on the Front Royal Pike, drove back Federal pickets at the Opequon River crossing (Parkins Mill Battery) around 8:30 a.m., and engaged in cavalry skirmishes at Hoge Run around 9:30 a.m.[12] Johnson's advance stalled under fire from Fort Milroy's heavy guns shortly before noon, and skirmishing and artillery engagements commended afterward with Federal artillery located on the hill near Hollinsworth Mill.

Having feared exactly this type of a scenario, General-in-chief Henry W. Halleck had asked Schenck to order Milroy to fall back from Winchester to Harpers Ferry.

Milroy had previously decided to disregard concerns from Washington because he was confident that the strength of his fortifications would allow his garrison to withstand an assault or a siege.

That afternoon, having reached Berryville, Rodes' Division and Jenkins' cavalry brigade attempted to capture McReynolds' Brigade, but, alerted to the Confederate movement by the firing of signal guns by Milroy's main force in Winchester, McReynolds withdrew to Winchester, where his force occupied the Star Fort north of town.

Within the Federal forts, Milroy and his sub-commanders believed that the Confederates had been repulsed from Winchester, still seemingly unaware they were now totally surrounded and cut off, with the additional problem of an entire division (Rodes') occupying their primary escape route north.

The twenty guns fired for 45 minutes, while Hays stealthily advanced his Louisiana brigade through the corn and wheat fields at the base of Apple Pie Ridge.

[16] Hays was supported in the attack by Smith's and Avery's brigade, and Early consolidated his line on West Fort (or Flint) Ridge, but darkness prevented further gains.

That evening, Ewell located his Corps Headquarters at the Bowers' House, while Early's Division pounded away at Milroy's main fort in an artillery duel well into the night.

Near dawn on June 15, Johnson's skirmishers encountered the head of Milroy's retreating column near the intersection of the Valley Pike and old Charles Town road.

At some point Milroy's horse was shot out from under him, and the division as a whole scattered in various directions to the northwest, north, and northeast, with some small groups even managing to escape covertly to the southeast toward and through Manassas Gap into Federally controlled territory.

Captain Palmer summarized the Union losses at a total of 4,443 for 1st, 2nd and 3rd Brigades from the 2nd Division, VIII Corps including all independent attachments.

It's no wonder that Confederate artillerist Maj. Robert Stiles wrote, "This battle of Winchester ... was one of the most perfect pieces of work the Army of Northern Virginia ever did."

[22] Additionally, the Confederates captured a great quantity of food, clothing, small arms ammunition and medical stores in Winchester.

Following this battle, a Court of Inquiry was held, and both President Abraham Lincoln and Halleck desired to know who disobeyed the orders to "evacuate Winchester".

Milroy was exonerated and claimed that his brilliant defensive action at Winchester was instrumental in causing the timing of the Battle of Gettysburg, leading to the overall Union victory for the campaign.

[24] Immediately following the battle, Ewell dispatched the entire Corps cavalry brigade under Jenkins on a raid to Chambersburg, Pennsylvania, to forage and reconnoiter.

Topographer Jedediah Hotchkiss then commenced an all day survey,[16] creating his now famous map of the battle which appears at the head of this article.

Early succeeded, where Lee failed twice at Sharpsburg and Gettysburg, and shelled Fort Stevens in Washington, D.C. During the Second Battle of Winchester, two Union enlisted men and one officer received the Medal of Honor for their actions.