Northern Virginia (1861)

At the outbreak of the American Civil War, McKee immediately worked to recruit a company of volunteers from the Lancaster area and was elected captain. His company was enrolled as Company C in the 2nd Wisconsin Infantry Regiment.^[2]

The 2nd Wisconsin Infantry was assigned to the brigade of Colonel William Tecumseh Sherman in the Army of Northeastern Virginia. They joined the march into Virginia in the Summer of 1861, and on July 21, they participated in the First Battle of Bull Run.^[4]: 439 In the morning phase of the battle, they were part of Sherman's successful flanking attack which destabilized the Confederate left.^[4]: 440

The Confederates, however, re-established their defenses further south, with reinforcements. In the disorganized afternoon assault against the Confederate defenses, the 2nd Wisconsin received friendly fire while assaulting an enemy cannon, and attempted to withdraw, becoming lost and intermingled in other disorganized regiments.^[4]: 440 Masses of Union soldiers fled the field. The 2nd Wisconsin attempted to cross the stone bridge, back to the east side of the Bull Run, but had to wade through the water as the bridge was blocked by broken artillery.^[4]: 441 The regiment was able to collect themselves near Centreville, Virginia. Since none of the field officers were present, the regiment elected Captain McKee to lead the march back toward Washington, D.C.^{[2][4]: 441} McKee wrote an account of the casualties of his company after the battle.^[5]

The regiment spent the remainder of the year in camp near Washington, building fortifications and drilling. They received visits from President Abraham Lincoln, Secretary of State William H. Seward, and Wisconsin Governor Alexander Randall.^[4]: 442

Island Number Ten (Spring 1862)

On March 26, 1862, McKee was commissioned lieutenant colonel for the new 15th Wisconsin Infantry Regiment (The "Scandinavian Regiment").^[1] McKee met the regiment at Island Number Ten on the Mississippi River, near New Madrid, Missouri, after the battle there.^[2] The 15th Wisconsin Infantry had been left to garrison the island, due to the large stores of ammunition at the site.^[6]: 615

Kentucky campaign (Fall 1862)

In June, the 15th Wisconsin departed Island Number 10, marching to Union City, Tennessee, and joining the division of General Robert Byington Mitchell.^[6]: 615 The division marched through western Tennessee, arriving at Florence, Alabama, on August 24. At that point, however, all Union forces in the area were recalled to Louisville, Kentucky, to head off the attack of General Braxton Bragg, who had launched an offensive through central Tennessee into Kentucky.^[6]: 616 They arrived tired and hungry on September 26.^[6]: 616 After a few days, the Union Army marched out to confront Bragg and met him near Perryville, Kentucky.

The Battle of Perryville occurred on October 8, 1862, but the 15th Wisconsin Infantry and its division was located at a position south of the main battlefield. They remained in support of a cannon battery through the morning, until a small Confederate detachment approached their position. The Union force easily repelled the Confederate attack, with the 15th Wisconsin Infantry joining in the skirmish.^[6]: 616 After briefly pursuing Bragg, the Union army turned to consolidating their position.

Middle Tennessee (Winter 1862)

In early November, Lt. Colonel McKee was put in command of an expedition to reconnoiter forage and terrain, and hunt Confederate guerillas. He captured 47 prisoners, destroyed about 100 small arms, and burned two homes and a distillery which he believed were providing refuge to guerilla parties.^[6]: 617 Colonel William Carlin complimented McKee on the expedition, saying, "This handsome little success, which shows what good infantry can do under an enterprising leader, reflects much credit on all who were engaged in it."^[7]: 12

Following the expedition, the 15th Wisconsin Infantry returned to Nashville, Tennessee. The Army had been reorganized in the meantime, and the 15th Wisconsin Infantry was now organized in the division of Brigadier General Jefferson C. Davis, in the right wing of the Army of the Cumberland, under Major General Alexander McDowell McCook.^[6]: 618 The army set out against Bragg on December 26, meeting him near Murfreesboro, Tennessee. That day, a Confederate cannon battery was identified on a formidable terrain feature known as Knob Gap, and Lieutenant Colonel McKee was ordered to lead a band of skirmishers to take the battery at all costs.^[6]: 618 McKee took one company from each regiment of the brigade and led them directly at the enemy cannons, through brush and over hills, until they were close enough to open fire. The brigade followed after them, sending the Confederates scattering, and taking possession of the guns.^[6]: 618

They camped at the gap, then continued their advance. On the morning of December 30, the two armies met in the opening phase of the Battle of Stones River. The 15th Wisconsin Infantry and their division were placed in the middle of the right wing of the Union line. McKee again commanded the skirmish line, encountering the enemy and clearing the advance for the brigade. The Union advance halted in the afternoon, then slept in position on the battlefield.^[6]: 619

On the morning of December 31, a Confederate attack on the Union right sent that division into retreat. Colonel Heg, commanding the 15th Wisconsin Infantry, sought to stabilize the line and ordered his regiment to turn right to avoid being flanked.^[6]: 620 They engaged in an intense firefight in this position, where McKee was shot in the forehead and killed. The regiment subsequently retreated, finding themselves nearly surrounded with enemy on three sides.^[6]: 620

McKee's body was recovered and sent to Lancaster for burial.^[2] His death was noted in the reports of Major General McCook, Brigadier General Davis, and Colonel Carlin.^{[7]: 258, 265, 281}