Emmett MacDonald practiced law in St. Louis and joined the Missouri Volunteer Militia in the First Military District (St. Louis) under the command of Brigadier General Daniel Frost before the Civil War. In November 1860, Frost received orders from Missouri Governor Robert Stewart to restore order along the Missouri border from raiding parties of Kansas Jayhawkers. MacDonald and approximately 650 militiamen from St. Louis and Jefferson City traveled to Fort Scott, Kansas and then Vernon County, Missouri to patrol the region.

MacDonald returned to St. Louis sometime in late April 1861. He was then captured by Nathaniel Lyon at Camp Jackson on May 10, 1861. He refused parole, but was eventually released by the court system. MacDonald then joined the Missouri State Guard and participated in the battles of Carthage, Wilson’s Creek, and Lexington. He joined the 3rd Battery, Missouri Light Artillery in October 1861, when it was organized from various units of the Missouri State Guard near Osceola, Missouri; the battery was mustered into Confederate service on January 28, 1862.

At the Battle of Pea Ridge, the battery, under the command of Captain MacDonald, fired over 700 artillery rounds before being forced to retreat; the unit also saw action at the siege of Corinth, Mississippi. The 3rd Battery was reorganized on September 10, 1862, and a new captain was elected when MacDonald failed to return to the unit (he had been authorized to recruit a cavalry regiment in the Trans-Mississippi Theater).

By November 1862, then Colonel MacDonald had recruited five companies and organized them into a cavalry battalion. After participating in the fighting at Cane Hill and Prairie Grove, Arkansas, MacDonald’s Battalion joined Gen. John S. Marmaduke’s raid into Missouri. The command fought at Springfield on January 8, and three days later at Hartville, Missouri. Colonel MacDonald was killed by a Minie bullet to the left thigh while leading a charge at Hartville, and was later buried in Bellefontaine Cemetery in St. Louis.