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“You have all read of ‘wars, & horrors of war,’ among christianized civilized, & savages,” a weary Confederate observed from western Missouri in August 1862, “but I cannot convey to you the horrors of this one.”

Even with the Rebel army pushed out of Missouri, the Confederate woman’s town of Warrensburg remained a perfect “thoroughfare” for Union soldiers, jayhawkers, bushwhackers and marauders of every stripe. First one side and then the other occupied the place, with its citizens caught in the middle. Trade was suspended; businesses collapsed. Civil law could not be enforced, and the flight of many residents gave the appearance of abandonment and desolation.

Her lament could be heard in nearly every part of the Trans-Mississippi. A combination of hopelessness, uncertainty and terror defined peoples’ lives. Even in a state supposedly controlled by the Union Army, Missourians experienced “war in earnest.” In September 1862, a band of 200 Rebel guerrillas barged into the northeastern town of Palmyra. Union troops had shot two and captured six others in an earlier skirmish, and the Rebels wanted retribution. During the three hours they occupied Palmyra, the raiders released 51 prisoners from the town jail, plundered the provost marshal’s office, rounded up every breathing horse, confiscated weapons and even kidnapped an elderly citizen. They scarcely bothered with a small number of Union troops who barricaded themselves in some stout brick buildings.

A few weeks later, the raid’s leader, Joseph C. Porter, received an ultimatum from the Federals. If Porter did not return the kidnapped citizen unharmed within 10 days, 10 of his men being held prisoner would be shot. Unfortunately, the old man was already dead. Porter had ordered him released shortly after the raid, but his men had murdered him. With no prisoner to be returned, the 10 Rebels—only three of whom had ever served with Porter—met their promised fate on October 18. Missourians on both sides were horrified as word of the “Palmyra Massacre” spread. Apparently one of the executed “guerrillas” was as elderly as the slain Unionist; another victim was a retarded boy.

Governor Hamilton Gamble made no complaint. Desperate to rid his state of Rebel guerrillas by any means, he even offered cash bounties for the capture of particularly nasty characters. Alfred Boland, who operated in the vicinity of Forsyth, was worth $5,000, dead or alive. Two men, one of them a paroled Confederate soldier, went looking for Boland in December 1862. Tracking the “bloodthirsty villain” to his lair, they lured Boland into a trap and shot him, though some accounts say they struck the guerrilla from behind with a plowshare. Legend says the bounty hunters decided it would be easier to sever the guerrilla’s head (all that was required for identification) than to lug his body halfway across the state to Jefferson City, where they would claim the reward. More reliable evidence has them carrying the whole corpse 12 miles to Forsyth and putting it on public display. Hundreds of people “gloated” over the remains of the man whose gang had “committed every [possible] atrocity.” The corpse was then sent to the state capital. Besides collecting their $5,000, the bounty hunters also received commissions as officers (captain and lieutenant, respectively) in the 11th Missouri Cavalry.

Gamble’s bounty system grew in part from his conviction that the “kind hearted” President Lincoln commuted or reduced the death sentences of too many convicted guerrillas. Gamble wanted authority given either to him or to district military commanders to endorse death sentences. Lincoln refused to relinquish his prerogative, but the issue sparked debate in the president’s cabinet. Sympathizing with Gamble, Attorney General Edward Bates told Lincoln, “We are habitually bullied by the enemy and constantly yield to his threats.” The government, he argued, must act more forcefully against Rebel guerrillas.

Bates also made an astonishing—and frighteningly accurate—prediction. Should local authorities be denied more control over executions, he warned, the government could expect to see fewer guerrilla trials, perhaps none. Fearful that guilty verdicts might be overturned, army commanders would embrace Maj. Gen. Henry Halleck’s doctrine of execution without trial. “I shrewdly suspect that your best officers are already acting upon that idea,” the attorney general told Gamble. “And upon the whole, I am not sure that it is not for the best; for I am persuaded that speed is quite as necessary as the fact of the punishment of such marauders.”

One can imagine how swiftly word of the attorney general’s view spread through the Union Army. Senior commanders and junior officers alike chose their own means of stamping out rebellion. Even financial assessments, which had been used for more than a year in Missouri, became opportunities for physical intimidation and an excuse for outright plundering. Colonel Lewis Merrill, the senior commander in northeastern Missouri, announced in September a dual program of reparation payments and public executions in his district. It is not clear if accused guerrillas received lawful trials, but Merrill, an 1855 graduate of West Point who had served earlier as Maj. Gen. John Frémont’s chief of staff, ordered their execution carried out with “due form and solemnity.” He hoped a few such examples would end guerrilla resistance, but he vowed to continue the policy until achieving his ends.

The state militia also felt free to act as judge and jury. “We captured a bushwhacker yesterday on the way coming here,” a militia lieutenant confided in a private letter. “He had been tried by drumhead court marshall and condemned to death[;] he will be executed in about one hour[;] his grave [he] is now diging.” The prisoner deserved no mercy, the lieutenant explained, as he was known to have helped “massacre” the teamsters of a supply train. Another scouting party shot two captured guerrillas without even a perfunctory trial, and this after forcing the men to lead them to the gang’s camp. “We take no pleasure in putting to death any one in human shape,” declared one militia captain, “but know of no other way of ridding our country of midnight assassins.”

When The New York Times, an avowed critic of Republican policies, accused Canadian-born Colonel John McNeil of “butchery” in executing 15 Missouri guerrillas after a perfunctory “trial,” McNeil’s provost marshal exploded in righteous anger. People back home did not understand the murderous conditions faced by soldiers and Unionists in this war, Colonel William R. Strachan said bitterly. “Had one half the severity practiced by Rebels on the Union men of Tennessee, Arkansas, and Missouri been meted out in return to them, every trace of treason would ere this have been abolished from our land.” Thousands of these scoundrels hounded honest folk, Strachan insisted, and their “long list of crimes…would make even fiends in hell shudder.” Besides, the colonel emphasized, the policies for dealing with guerrillas in Missouri, having been initiated by Henry Halleck and Brig. Gen. John M. Schofield, were longstanding.

Frustration often spawned callous disregard for human life and suffering. A Pennsylvania-born soldier felt totally justified in shooting captured guerrillas in southeastern Missouri. “They are a set of murderers and are not fit to live to encumber society,” he told his wife plainly. His attitude became even more ingrained one day in February 1863, when he came across a woman crying beside the corpse of her guerrilla husband, who had been taken from their house and shot on the open road. Any instinctive sympathy the scene might have aroused was dashed by the woman’s response to the soldiers. “She was no better than he,” the Pennsylvanian reported, “for she kept on swearing vengeance against the Federals and said she would make them kiss his blood….It looks hard to me to see a man shot and his wife and children left alone,” he admitted, “but these men are the ones that keep up the cruelties that are continually being practiced in this part of Missouri.”

The Federals destroyed Rebel property as a form of chastisement. The holdings of known bushwhackers had no chance of surviving, and their supporters suffered if the guerrillas themselves could not be hurt. It sometimes became a game of escalating revenge. When army expeditions failed to capture their elusive prey, they contented themselves with burning Rebel homes. If guerrillas burned a Unionist home in response, the army burned two more Rebel homes. Rebel rendezvous sites became favorite targets. Insofar as Rebels often gathered at mills, taverns or stores, their destruction—more than the torching of a single home— could undermine the guerrilla network and intimidate the neighboring populace. For a rural community to lose a mill, for instance, could be a financial blow that caused people to reconsider the price of disloyalty. Likewise, cavalry patrols sustained themselves by demanding their meals and water for their mounts from Rebel households. Add to this the assessments and routine confiscation of property, and it was reasonable to think the Confederates would eventually forsake their partisans.

The army also used covert methods. Army commanders assigned scouts in civilian dress to circulate through Rebel neighborhoods not only to locate guerrilla camps, as was already being done, but also to gather evidence against citizens who aided the irregulars. Provost marshals issued “detective” credentials with the same goal in mind. A team of two detectives in western Missouri even “played off as bushwhackers” to incriminate one man. On visiting his home, they flashed a secret sign known to be used by local guerrillas. The man responded and, as the detectives gained his confidence, he talked freely of having often sheltered Rebels. “He fed us and our horses and told us which way to get out,” they subsequently testified at the man’s trial. “We pretended that we wanted to get over the river to find out where [William Clarke] Quantrill was.” He told them where to cross and gave them the names of two men on the other side who would further assist them.

Banishment, though not widely applied, became another option. General Benjamin Loan used this threat to silence dissent around Lexington. He rounded up hundreds of men who spoke publicly against the United States in the latter part of 1862. “We do not know what minute we will be arrested and banished from the state,” a Confederate citizen revealed in his diary. The “Tiranical” Loan had established “a perfect reign of terror.” Unionists thought the policy long overdue. “If the government had adopted the plan…of banishing all Rebel sympathizers…a year ago,” judged one Missourian in June 1863, “the war would now be a great deal nearer a close than it is.”

U.S. military commissions continued to do a brisk business, as did some civil courts that claimed jurisdiction in guerrilla cases. The odds were getting longer for acquittal, but a fair number of defendants still managed to escape the gallows. The fate of Jacob Fowler and 10 members of his guerrilla band seemed certain. Found guilty of plundering Unionist property in Missouri and of wounding several Union soldiers on an unarmed steamboat, all were sentenced to die. Several of the men wiggled free of the hangman’s noose, however, when the district commander found technical irregularities in the commission’s decision. Fowler’s testimony saved two men when he acknowledged that they had not participated in the crimes. Almost shockingly, Fowler himself received a prison term rather than a death sentence. He swore that he had ordered his band of some 50 guerrillas not to fire on the steamboat. Two of his men, subsequently released, vouched for that statement. One of these men also testified that Fowler, though guilty of plundering, had refused to drive the Unionists from their homes, as some of his followers had wanted to do.

Yet these efforts to dispense justice yielded two fearful realizations. First, hours of testimony in scores of trials confirmed the utter intransigence of Rebel guerrillas. Second, and far worse, the evidence showed a distinctly new type of guerrilla emerging by the end of 1862. Common outlaws, deserters and other misfits were exploiting the chaos of war for personal gain. Scattered complaints about “predatory bands,” roaming gangs of “banditti” and other miscreants could be heard as early as the spring of 1861, but more of them, in larger numbers, were now operating. They sometimes claimed to be loyal Confederates or Unionists, but most of them had no allegiance other than to themselves. “It is an old saying…that the ‘Devil is fond of fishing in muddy waters,’” an Arkansan observed in January 1862, “and as soon as war stired up the mud of confusion you see devils turn out in droves like avenging Wolves….I predict if the war lasts 12 months longer the country will be completely over run with vagabonds and [they] will have to be killed in some way.”

Curiously, this turn in the guerrilla war renewed Unionist hopes. It seemed likely, they reasoned, that even Confederate civilians would recoil from the excesses of these mutant guerrillas. The additional wave of violence and destruction could stir resentment against the Rebel government for failing to protect its citizenry. The outlaws might tarnish the reputation of all Rebel guerrillas and indisputably associate their cause with lawlessness. “I am sure the people here are tired—very tired—of the war,” a Unionist reflected near Mexico, Mo., center of some of the state’s worst guerrilla violence. “I am confident the ‘bushwhacker’ will not have much aid or comfort in this part of the state again.”

The complexity of the situation only made it more difficult for the two sides to agree on an acceptable definition of a “guerrilla,” and this had begun to gnaw at Henry Halleck. He had been satisfied with his own handling of guerrillas in the Trans-Mississippi, but by August 1862, as general-in-chief, he came to understand both the scope of the guerrilla problem and the complex legal issues it entailed. Wishing to make sure the United States held the moral and legal high ground, he turned to Dr. Francis Lieber for advice. The German-born Lieber had taught history and political philosophy for 21 years at South Carolina College before moving to New York’s Columbia College in 1856. The Southern and Northern residences produced a family with divided loyalties. One of Lieber’s three sons had already died in Confederate service, and a son in the Union Army had lost an arm. The professor, who felt passionately about the evil of both slavery and secession, had never wavered in his devotion to the Union or ceased to ridicule the “many hypocrasies or absurdidies” of the South. He also called the guerrilla war an affront to international law.

Henry Halleck

Being personally acquainted with the professor, Halleck recognized a kindred spirit. “The Rebel authorities claim the right to send men, in the garb of peaceful citizens, to waylay and attack our troops, to burn bridges and houses, and to destroy property and persons within our lines,” he told Lieber. “They demand that such persons be treated as ordinary belligerents…[with] the same rights as other prisoners of war.” Halleck asked what Lieber thought of this reasoning. Did it have any legal basis?

Lieber’s analysis reflected the elusive and controversial nature of the subject, addressed every issue plaguing Halleck and countered any defense the Confederates might muster. He defined nearly a dozen types of irregular warfare but relegated most Southerners to the general category of “war-rebel.” These men posed the “greatest danger” to an occupying army, Lieber declared, and should be treated with the “utmost rigor of the military law.” It mattered not if they organized and fought on their own initiative or had been “secretly called upon” by the government. Civilized governments should not employ or recognize them. Both the “bushwhacker” and “guerrillaman” qualified as war-rebels, and Lieber made little distinction between them. The bushwhacker acted more often alone, as an “armed prowler” or “simple assassin,” but both were brigands. Neither could claim legitimacy, even if their government had called upon “the people to infest the bushes and commit homicides.”

Lieber conceded that difficulties might arise when distinguishing partisans from guerrillas, which had been the thorniest issue facing Union soldiers in the field. As long as suspected “guerrillamen” conducted themselves as partisans and were captured “in fair fight and open warfare,” they should be treated as soldiers until proved guilty of some crime, such as murder or pillage. However, Lieber cautioned, the Army should not tolerate “small bodies of armed country people” who resorted to “occasional fighting and the occasional assuming of peaceful habits, and to brigandage.” No circumstances could justify their actions.

Remarkably, Lieber claimed he had not meant to suggest how these general “rules of action” should be applied to “evil-doers” in the present war. That must be decided by the government’s leaders. He could only say that no society, either in peace or war, could allow “assassination, robbery, and devastation” to go unpunished. In wartime, such neglect could have “disastrous consequences which might change the very issue of the war.”

Halleck immediately distributed the guide to his armies to identify and treat Rebel guerrillas, but Lieber was just warming up. Concerned he had addressed only the most immediate questions raised by Rebel guerrillas, he urged Halleck to issue another, broader “set of rules” to define the conduct of the general war.

In response, Halleck appointed a five-man committee, including Lieber, to produce the recommended document. The resulting Lieber Code was issued to the Army as General Order No. 100 in August 1863. It has been rightly hailed as the first ethical guideline for the conduct of war issued by a democratic state, but that should not obscure Lieber’s more immediate and quite practical goals. He meant to enhance the Union Army’s legal authority and maximize its ability to crush the rebellion. “Military necessity” became the code’s operating principle, and while Lieber was careful to emphasize the need for soldiers on both sides to treat combatants and noncombatants alike with compassion, his edicts defended the use of retaliation “to obtain great ends of state” and to battle “against wrong.” Nations waging war in a “noble cause” must base their actions on the “principles of justice, faith, and honor,” but “the more vigorously” they pursued such wars, “the better…for humanity.”

The Confederates, quite naturally, denounced these “laws and usages of war” as Yankee propaganda, a “confused, unassorted and undiscriminating” mess. Secretary of War James A. Seddon dismissed Lieber as a foreigner who understood neither the American legal system nor American military traditions. He pointed especially to the principle of military necessity, which Seddon claimed was intended to defend the “acts of atrocity and violence” committed by Union troops. The Confederate States, he said, would not allow the United States to “frame mischief into a code.”

It is more difficult to judge the practical impact of Lieber’s labors on the Union Army. Neither officers nor men said much about the new orders. Lieber himself worried about the applicability of the section on guerrillas for soldiers in the field. Its usefulness must necessarily be “much diminished by the fact that the soldier generally decides these cases for himself,” he admitted. As for the broader reaches of the Lieber Code, some Union officers dismissed it as a “defense of radical abolition principles.” They called Lieber a “very learned” but dangerous “bookworm.” His code, when combined with Abraham Lincoln’s recently enacted emancipation program, “only served to unite the people of the Rebel states, and to give strength to the Rebellion.”

Certainly for the moment, codes, courts and commissions would not resolve the guerrilla war in Missouri. Only relentless pressure, as even Lincoln had come to understand, could achieve that end. As Rebel guerrillas emerged from winter hibernation in 1863, the internal threat to Missouri became unparalleled. It may as well have been the summer of 1861. In April 1863, a veteran Union cavalryman admitted, “Missouri since the commencement of the war never was so overrun with Guerrillas as it is at the present time.” Worse still, no one knew how to slow the flood. “There is a terrible state of affairs here,” a Union officer conceded, “the more I see of it the more complicated it seems.”

Adapted from A Savage Conflict: The Decisive Role of Guerrillas in the American Civil War by Daniel E. Sutherland (University of North Carolina Press, July 2009).

Originally published in the September 2009 issue of America’s Civil War.