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Guerrillas in the American Civil War
Irregular warfare in the American Civil War followed the patterns of irregular warfare in 19th century Europe. Structurally, irregular warfare can be divided into three different types conducted during the Civil War: 'People's War', 'partisan warfare', and 'raiding warfare'. The concept of 'People's war,' first described by Clausewitz in On War, was the closest example of a mass guerrilla movement in the era. In general, this type of irregular warfare was conducted in the hinterland of the Border States (Missouri, Arkansas, Tennessee, Kentucky, and northwestern Virginia), and was marked by a vicious neighbor against neighbor quality. One such example was the opposing irregular forces operating in Missouri and northern Arkansas from 1862 to 1865, most of which were pro-Confederate or pro-Union in name only and preyed on civilians and isolated military forces of both sides with little regard of politics. From these semi-organized guerrillas, several groups formed and were given some measure of legitimacy by their governments. Quantrill's Raiders, who terrorized pro-Union civilians and fought Federal troops in large areas of Missouri and Kansas, was one such unit. Another notorious unit, with debatable ties to the Confederate military, was led by Champ Ferguson along the Kentucky-Tennessee border. Ferguson became one of the only figures of Confederate cause to be executed after the war. Dozens of other small, localized bands terrorized the countryside throughout the border region during the war, bringing total war to the area that lasted until the end of the Civil War and, in some areas, beyond.

Partisan warfare, in contrast, more closely resembles Commando operations of the 20th century. Partisans were small units of conventional forces, controlled and organized by a military force for operations behind enemy lines. The 1862 Partisan Ranger Act passed by the Confederate Congress authorized the formation of these units and gave them legitimacy, which placed them in a different category than the common 'bushwhacker' or 'guerrilla'. John Singleton Mosby formed a partisan unit which was very effective in tying down Federal forces behind Union lines in northern Virginia in the last two years of the war.

Lastly, deep raids by conventional cavalry forces were often considered 'irregular' in nature. The "Partisan Brigades" of Nathan Bedford Forrest and John Hunt Morgan operated as part of the cavalry forces of the Confederate Army of Tennessee in 1862 and 1863. They were given specific missions to destroy logistical hubs, railroad bridges, and other strategic targets to support the greater mission of the Army of Tennessee. By mid-1863, with the destruction of Morgan's raiders during the Great Raid of 1863, the Confederacy conducted few deep cavalry raids in the latter years of the war, mostly due to the losses in experienced horsemen and the offensive operations of the Union army. Federal cavalry conducted several successful raids during the war but in general used their cavalry forces in a more conventional role. A good exception was the 1863 Grierson's Raid, which did much to set the stage for General Ulysses S. Grant's victory during the Vicksburg Campaign.

Federal counter-guerrilla operations were very successful in preventing the success of Confederate guerrilla warfare. In Arkansas, Federal forces used a wide variety of strategies to defeat irregulars. These included the use of Arkansas Unionist forces as anti-guerrilla troops, the use of riverine forces such as gunboats to control the waterways, and the provost marshal military law enforcement system to spy on suspected guerrillas and to imprison those captured. Against Confederate raiders, the Federal army developed an effective cavalry themselves and reinforced that system by a large number of blockhouses and fortification to defend strategic targets.

However, Federal attempts to defeat Mosby's Partisan Rangers fell short of success due to Mosby's use of very small units (10–15 men) operating in areas considered friendly to the Rebel cause. Another regiment known as the "Thomas Legion," consisting of white and anti-Union Cherokee Indians, morphed into a guerrilla force and continued fighting in the remote mountain back-country of western North Carolina for a month after Lee's surrender at Appomattox. That unit was never completely suppressed by Union forces, but voluntarily ceased hostilities after capturing the town of Waynesville on May 10, 1865.

In the late 20th century several historians have focused on the non-use of guerrilla warfare to prolong the war. Near the end of the war, there were those in the Confederate government, notably Jefferson Davis who advocated continuing the southern fight as a guerrilla conflict. He was opposed by generals such as Robert E. Lee who ultimately believed that surrender and reconciliation were better than guerrilla warfare.