Following the Union's capture of Tucson in May 1862, Swilling's company retreated and he became a civilian employee of the United States Army, first as a dispatch rider between General James Carleton's California Column and Union forces up the Rio Grande, and later as a scout in an anti-Apache campaign. He was involved in the campaign to take Mesilla which ended with a Union takeover of Confederate Arizona's capital. Near the end of that employment, he encountered the Joseph R. Walker exploratory party near Pinos Altos when Swilling led the capture of the famous Apache chief Mangas Coloradas.