[1][2] Murphy entered military service around 1861 when the 8th Wisconsin Infantry Regiment was created around September 13, but wouldn't see any major operations until an entire year later at the Battle of Iuka.

During the battle, Murphy was stationed to guard a small supply depot, but on September 14, he applied a scorched earth policy at the depot, and the pursuing Confederates doused the fire in time to capture a large amount of supplies, and Murphy was captured himself in his pajamas.

[4] Later in the same year, Murphy was put in charge of another supply depot stationed at Holly Springs, Mississippi[2][5] when Confederate general Earl Van Dorn led a raid on the Union forces stationed there and defeated them, which took a heavy toll on Grant's Vicksburg campaign, and Murphy was dismissed from the army without a court-martial.

[1] Murphy wrote to Abraham Lincoln to ask for a court-martial or hearing, but Adjudant-General Joseph Holt concluded that his dismissal was reasonable.

Murphy attempted for the next fifteen years to get a hearing but failed in the end.