In the years leading up to the
American Civil War, Malloy became active with the
Wisconsin militia and helped to drill Sauk County volunteers in
Baraboo, Wisconsin. At the outbreak of the war, Malloy's trainees became part of the "Madison Guards" militia company which joined the
1st Wisconsin Infantry Regiment. Malloy remained in Baraboo to organize a full company from the surrounding area and was elected captain of that company. Malloy led his company to
Camp Randall, in Madison, where they were enrolled as Company A of the
6th Wisconsin Infantry Regiment.
Irish brigade (Spring 1862Winter 1864) That December, Malloy was promoted to
lieutenant colonel for the newly organized
17th Wisconsin Infantry Regiment—the "Irish Brigade". The 17th Wisconsin was organized at Camp Randall and mustered into service in March 1862. With the 17th Wisconsin, Malloy moved to the
western theater of the war and participated in the sieges of
Corinth and
Vicksburg in Mississippi. Before Vicksburg, in November 1862, Malloy was promoted to
colonel of the regiment, following the resignation of Colonel
John L. Doran. Malloy and the 17th Wisconsin re-enlisted as a veteran regiment in January 1864, earning a month-long furlough in Wisconsin. Upon their return, they joined General
William Tecumseh Sherman's
Atlanta campaign. They were attached to
XVII Army Corps at
Huntsville, Alabama, and were organized into the 3rd brigade of the 3rd division of the corps. Malloy was placed in command of the brigade, which also included a battalion of men detached from the 14th Wisconsin, 81st Illinois, and 95th Illinois infantry regiments. Colonel Malloy's own account of the battle can be found in the Official War Records, Series 1, Volume 47, Part 1, item 266.
Final months (Summer 1865) After the reunion with Sherman's army, Malloy resumed command of the 17th Wisconsin Infantry for the remaining days of the war. They marched to
Raleigh, North Carolina, and were camped there when they received word of the surrenders of the Confederate
Army of Northern Virginia and the
Army of Tennessee, effectively ending the war. ==Postbellum career==