In the words of historian James G. Randall: "No president has carried the power of presidential edict and executive order (independently of Congress) so far as [Lincoln] did.... It would not be easy to state what Lincoln conceived to be the limit of his powers." In the 80 days that elapsed between Lincoln's April 1861 call for troops--the beginning of the Civil War--and the official convening of Congress in special session on July 4, 1861, he performed a whole series of important acts by sheer assumption of presidential power. Lincoln, without congressional approval, called forth the militia to "suppress said combinations," which he ordered "to disperse and retire peacefully" to their homes. He increased the size of the Army and Navy, expended funds for the purchase of weapons, instituted a blockade--an act of war--and suspended the precious writ of habeas corpus, all without congressional approval. Lincoln termed these actions not the declaration of "civil war," but rather the suppression of rebellion. Only Congress is constitutionally empowered to declare war, but suppression of rebellion has been recognized as an executive function, for which the prerogative of setting aside civil procedures has been placed in the President's hands.

From David Greenberg's History Lesson columns in Slate, 11/30/01 and 12/5/01:

Civil libertarians are crying foul over the indefinite detention of hundreds of Sept. 11 suspects and plans to try accused terrorists in military tribunals. In defense, some Bush administration loyalists cite another wartime leader who locked up civilians and resorted to army courts, Abraham Lincoln—even though Lincoln faced a radically different situation, and, more important, his civil liberties record stands as a rare blot on his reputation.

First a definition: The Latin phrase habeas corpus means "you have the body." The privilege of the writ of habeas corpus refers to a common-law tradition that establishes a person's right to appear before a judge before being imprisoned. When a judge issues the writ, he commands a government official to bring a prisoner before the court so he can assess the legality of the prisoner's detention. When the privilege of the writ is suspended, the prisoner is denied the right to secure such a writ and therefore can be held without trial indefinitely. Habeas corpus is the only common-law tradition enshrined in the Constitution, which also explicitly defines when it can be overridden. Article I, Section 9 of the Constitution says, "The privilege of the writ of habeas corpus shall not be suspended, unless when in cases of rebellion or invasion the public safety may require it."

Several times during the war, Lincoln or his Cabinet officers issued orders suspending the writ. The first came early in his presidency. Lincoln had been in office for barely a month when Confederate troops attacked the federal garrison at Fort Sumter in April 1861, starting the Civil War. One of his immediate concerns was how to keep an unobstructed route between Washington, D.C., and the North. He worried that if Maryland joined Virginia and seceded from the Union, the nation's capital would be stranded amid hostile states. On April 19, 20,000 Confederate sympathizers in Baltimore tried to stop Union troops from traveling from one train station to another en route to Washington, causing a riot. So on April 27 Lincoln suspended the habeas corpus privilege on points along the Philadelphia-Washington route. That meant Union generals could arrest and detain without trial anyone in the area who threatened "public safety."

Controversy followed. The most explosive incident centered on John Merryman, a Marylander arrested for insurrectionary activities. Summarily jailed, Merryman petitioned for a habeas corpus writ, which Chief Justice Roger Taney granted. But the commanding officer at Fort McHenry, where Merryman was held, refused to release the prisoner, citing Lincoln's edict. With the army loyal to Lincoln, Taney couldn't enforce his order and railed against the president while Merryman stewed in jail for seven more weeks. After being freed, he was never tried.

The Merryman case and others like it ignited a debate over Lincoln's actions. Democrats argued they were unconstitutional. Taney noted that Article 1 of the Constitution, where habeas corpus is discussed, deals exclusively with congressional powers, meaning that Congress alone can authorize the privilege's suspension. Although correct, Taney's argument framed the debate around a legalistic and secondary issue, that of congressional versus presidential power. It skirted the question of whether the situation warranted a suspension of habeas corpus at all. Thus when in March 1863 Congress passed the Habeas Corpus Act, effectively endorsing Lincoln's actions, civil libertarians were stripped of their main argument....Where Democrats marshaled constitutional arguments against Lincoln's order, Republicans replied that in an emergency, only the president could act fast enough to protect the public safety. Lincoln himself took this line in a famous July 4, 1861, speech to Congress. He also, more memorably, used a pragmatic argument. "Are all the laws but one to go unexecuted," he chided his critics, "and the government itself go to pieces, lest that one be violated?" The phrase has been quoted ever since and even provided the title of a recent apologia by Chief Justice William Rehnquist for wartime suppression of freedoms.

Despite the rhetorical power of Lincoln's speech, there's no evidence the government would have gone to pieces. By the time he issued his April 27 order, Union troops had made their way through Baltimore, and it should have been clear that Washington wasn't going to be fatally isolated. As for dissuading Maryland from seceding, contemporaneous accounts suggest that whatever the administration's fears, no such move was imminent.

If Lincoln's Maryland actions were dubious, a wave of arrests the following summer under another habeas corpus suspension was downright indefensible. The wave began after Congress instituted the first-ever military draft in July 1862. Because the draft proved highly unpopular and hard to enforce, Secretary of War Edwin Stanton, at Lincoln's behest, issued sweeping orders on Aug. 8 suspending habeas corpus nationwide—the first time the writ was suspended beyond a narrowly defined emergency area. Stanton decreed that anyone "engaged, by act, speech, or writing, in discouraging volunteer enlistments, or in any way giving aid and comfort to the enemy, or in any other disloyal practice against the United States" was subject to arrest and trial "before a military commission."

The exceedingly broad mandate precipitated a civil liberties disaster. It allowed local sheriffs and constables to decide arbitrarily who was loyal or disloyal, without even considering the administration's main goal of enforcing the draft. At least 350 people were arrested in the following month, an all-time high. Some of the accused had done nothing worse than bad-mouth the president. (That was also true before Aug. 8. On Aug. 6, for example, Union Gen. Henry Halleck arrested one Missourian for saying, "[I] wouldn't wipe my ass with the stars and stripes.")

On Sept. 8, the federal official overseeing these arrests decreed that law enforcement agents were enforcing the Aug. 8 orders too stringently. It was evident that people were being arrested who posed no threat to the public safety. Thereafter, the arrests subsided. Still, Lincoln himself reiterated the suspension on Sept. 24, and arrests without trial continued. Overall between 10,000 and 15,000 people were incarcerated without a prompt trial. On balance, their detention almost certainly did not enhance American security nor hasten the Union victory....

The big difference between the Bush plan and Lincoln's plan is that while Bush intends to try mainly what the Supreme Court has called "enemy belligerents" in his military courts, Lincoln prosecuted American civilians....Lincoln's Army tribunals began operating just a few months after the Civil War began. Disorder was acute in border states such as Maryland and Missouri, which remained loyal to the republic but contained many citizens who sympathized with or aided the Confederate rebels. In Maryland, Lincoln sought to quell the chaos by suspending habeas corpus (as discussed in last week's "History Lesson"). But Missouri was more intractable. In June 1861, the state's governor declared war on the Union forces even as he swore his fidelity to the United States; a month later, all-out combat had consumed the state. Union Gen. John C. Frémont imposed martial law in August.

Martial law, which Army commanders impose on populations when regular governments cease to function, is not the same as military law. According to the Articles of War passed by Congress in 1806, only members of the armed forces can be tried under military law....The defendants who came before these tribunals weren't Confederate soldiers, who, when captured, typically became prisoners of war and weren't put on trial. Rather, the defendants in military court were mainly civilians suspected of aiding the rebels. Gen. Halleck explained the rationale: In Missouri, he said, those burning bridges or buildings weren't "armed and open enemies" but "pretended quiet citizens living on their farms." These civilian rebels couldn't be treated as prisoners of war, but neither could they be entrusted to the local courts, which Halleck deemed "very generally unreliable"—not least because so many locals were likely to sympathize with the South....

The military trials that became most controversial were those of civilians who lived in Union or border states. Their offenses—which were categorized, rather indiscriminately, as "treason," "conspiracy," "rebellion," or other similar crimes—included engaging in guerrilla warfare, spying, avoiding the draft, and even voicing disloyal opinions. These defendants often received less than full justice.

The problem wasn't that the tribunals were kangaroo courts. Staffed by military officers, they did abide by set procedures and sometimes acquitted defendants. Sentences were subject to review by senior officers, death penalties by the president himself. Lincoln himself spared many lives.

But as is typical of military justice, those procedures afforded fewer protections than those of civilian courts. Basic constitutional requirements were ignored. The Army courts had no juries, as the Constitution mandates. Nor did they require a unanimous vote to convict. A majority vote sufficed, except in capital cases, which required a two-thirds vote....

The most egregious violations of civilians' rights occurred in the North, where unreliable or ill-functioning civil courts could not be used as an excuse for resorting to military justice. One famous case involved Clement Vallandigham, an Ohio Democrat, former congressman, and leading "Copperhead," or Northern opponent of the war. A double victim, Vallandigham suffered from both the suspension of habeas corpus and the rough justice of military courts.

On May 1, 1863, Vallandigham delivered a fiery anti-war speech in Mount Vernon, Ohio, in which he attacked, among others, Gen. Ambrose Burnside, the military officer in charge of the region. A short-fused Burnside ordered Vallandigham's arrest. A few nights later, troops burst into Vallandigham's house in the wee hours and carried him away. Within days, an Army court sentenced him to jail for the rest of the war. Vallandigham petitioned a federal judge for a habeas corpus writ, but the judge noted that Lincoln had suspended the privilege. Vallandigham had in fact been trying to provoke just such a result, and he knew full well that Burnside was likely to come after him. He thus achieved his purposes: attaining martyrdom for himself and throwing Lincoln on the defensive.

The controversy deepened with the case of Lambdin Milligan, whom a military court in Indiana had sentenced to death for joining a pro-Confederate secret society called the Sons of Liberty. The Supreme Court, which in 1864 had declined to rule on Vallandigham's case, agreed in 1866 to hear Milligan's. In Ex Parte Milligan, Justice David Davis, delivering a majority opinion in Milligan's favor—which four justices joined and with which four others concurred in a separate opinion—strongly rebuked the government. Davis, who had been Lincoln's friend and campaign manager, held that military tribunals had no jurisdiction over civilians. Article III of the Constitution, he noted, mandates that courts be set up by Congress, and the Sixth Amendment guarantees the right to a jury trial.

Technically, the court didn't question Lincoln's suspension of habeas corpus since the Habeas Corpus Act passed by Congress in 1863 had removed the pressing constitutional questions surrounding that action. But it did order the lower court to give Milligan a writ for his freedom. More important, Davis' opinion included a passage about wartime encroachments on freedoms that became a touchstone for civil libertarians ever since:

The Constitution of the United States is a law for rulers and people, equally in war and in peace, and covers with the shield of its protection all classes of men, at all times, and under all circumstances. No doctrine, involving more pernicious consequences, was ever invented by the wit of man than that any of its provisions can be suspended during any of the great exigencies of government. Such a doctrine leads directly to anarchism or despotism.