The outbreak of the Civil War in April 1861 required Brannan either to join the southern rebellion or remain loyal to his country. He had grown up in a Southern city, his family had owned a slave, and he had spent much of his career in the South. Yet he had been exposed to nationalist influences while a boy working for Congress, while a young man studying at West Point, and while a professional soldier in the U.S. Army. Furthermore, his hometown was the nation's capital, which remained in Union hands. Leaving Key West, where he had spent three years, Brannan returned to Washington and accepted an appointment as a brigadier general of U.S. volunteers in September 1861. His first assignment involved maintaining the defenses of his native city that November.
Dan R. Frost, "Brannan, John Milton," American National Biography Online, February 2000,http://www.anb.org/articles/04/04-00140.html.