Lincoln was well aware of the dangers that festered in Maryland from his recent exposure to the assassination plans for his trip to D.C. just months before. Baltimore, Maryland's chief city was part of the Union in name only. The city was overflowing with secessionist sentiment, if Maryland stayed in the Union was still an issue very much up in the air. After Virginia seceded, and the Confederacy moving its capital to Richmond, the Confederacy was now literally in Lincoln's view. Confederate flags flew from the rooftops in Alexandria, directly across the Potomac from the Capital. Washington, D.C., was very near in open panic as rumors of a Confederate attack raced through the city, which was defended only by a disorganized, ragtag Union army lacking any effective leadership.
Racing to the capital was the 6th Massachusetts militia under the command of Benjamin Butler, an ambitious Massachusetts Democrat who had supported Jefferson Davis for the presidency in 1860. However, after the secession, Butler became an enthusiastic War Democrat, later a Republican. Commanding the first northern troops to reach Washington, as Butler's men passed through Baltimore on April 19th, they were taunted by pro-secession civilians known as "pug-uglies." According to William Safire in his Civil War novel Freedom, "their name came from the plug hats as well as from the spikes studded in the front of their boots, worn by the hoodlums to do greater injury with a kick." When the mob began to throw bricks, paving stones, and rocks, the troops fired. No one ever took responsibility for ordering or firing the first shot, but federal guns were turned on civilians armed with only clubs and stones. The following melee left at least twelve civilians dead and dozens more injured. Four soldiers were also killed. It was weeks before a real clash between armies resulted in as many casualties.
The governor of Maryland and the mayor of Baltimore demanded Lincoln to forbid any more federal troops to pass through the city, but Lincoln refused. That night Marylanders burned railroad bridges to prevent any more troops from moving through the state. Groups of "plug uglies" roamed over Maryland, assaulting travelers. The area was close to open anarchy. In Washington rumors of a secessionist mob intent on attacking and burning the city filled the air. For the moment, Maryland appeared to be on the verge of joining the Confederacy, which would completely surround the capital with rebellious states. When Lincoln met some of the wounded Massachusetts men, he as beyond worry, saying, "I don't believe there is any North. The (New York) Seventh Regiment is a myth. Rhode Island is not known in our geography any longer. You are the only Northern realities."
Lincoln could look out from the White House and see Confederate flags flying in Alexandria, and Confederate campfires burning at night. Baltimore was about to explode, and vastly fewer Union militiamen had arrived in the nation's capital than Lincoln and his staff had expected. With this atmosphere of fear and uncertainty, the president called a Cabinet meeting. One of the first decisions was a limited suspension of the writ of habeas corpus along the rail lines between Philadelphia and Washington, essentially targeting Maryland.
Habeas Corpus literally means "you have the body"; a writ of habeas corpus is issued by a court and orders the authority to release a person being held in custody. Derived from English law, it is an essential part of the Constitution, intended to protect individuals from arbitrary imprisonment. It protects everyone from being arrested and held without reasonable charges. It was and it on of the individual protections that separates America from monarchies and other governments in which soldiers or police can literally knock on your door and haul you away without explanation.
With the suspension of habeas corpus, Lincoln authorized General Scott to make arrests without specific charges to prevent secessionist Marylanders from interfering with communication between Washington and the rest of the Union. In the next few months, Baltimore's Mayor William Brown, the police chief, and nine members of the Maryland legislature were arrested to prevent them from voting to secede from the Union.
When an otherwise obscure secessionist named John Merryman was arrested, Chief Justice Roger Taney went into action. Taney, a Marylander himself and the author of the Dred Scott decision that could be said was the spark that started the war by making it "Un-Constitutional" according to Taney to limit the growth of slavery in any state, negating the Missouri Compromise. Taney issued a writ of habeas corpus for Merryman, demanding that authorities give a reason for his detention. The military refused, and Taney, who thought that Lincoln might have him arrested as well, issued an argument stating that only Congress could suspend the privilege of the writ and that Lincoln had broken the laws. Protection from arbitrary arrest became the first serious constitutional crisis of the war.
In an address to Congress in July, Lincoln responded to Taney by asking "whether all the laws, but one, were to go unexecuted, and the government itself to go to pieces, lest that one be violated?" In other words, if Taney was so worried about the Constitution, whey hadn't he done anything to prevent secession? Lincoln further argued that the Constitution states that "the Privileges of the Writ of Habeas Corpus shall not be suspended, unless when, in Cases of Rebellion or Invasion the public Safety may require it." The Constitution never specified which of the three branches of government could suspend the writ, so Lincoln argued that any one of the three equal branches could do so.
Twice more during the war Lincoln, suspended habeas corpus, including the suspension "throughout the United States" on September 24th, 1862. Although the records are somewhat unclear, it seems more than thirteen thousand Americans, most of them opposition Democrats were arrested during the war years, giving rise to the charge that Lincoln was a tyrant and dictator. However, one must take into consideration that he was following his Constitutional mandate to protect the Union and the Constitution of the United States. He was dealing with the biggest threat to both in history with those who wanted to tear it asunder even in Washington as well as surrounding the capital. Desperate means for desperate times are prudent. How would you suggest that it be done differently?