Beall served as a private under the legendary Stonewall Jackson for a brief period of time, but received a serious chest wound in October of 1861. He then buddied up to a nephew of Robert E. Lee's and got audiences with the President of the Confederacy, Jefferson Davis. Beall was soon given two small boats and a handful of men and granted the title of "acting master" in the Confederate Navy. But he was rarely provided with specific orders or assignments. Instead, Beall acted as a kind of "privateer," randomly appearing here and there to destroy a lighthouse, cut a telegraph wire or capture a trading vessel. As will be seen, the ambiguous nature of Beall’s position eventually carried over into his work.
Eventually, General Wister and five hundred men were sent out to capture Beall and whoever was with him. In November of 1863, Beall was placed in irons in Fort McHenry. But he was part of a prisoner exchange the following year and it wasn't long before Beall and twenty to thirty men dressed as ordinary citizens boarded the Philo Parsons. Beall casually chatted with the mate at the wheel as the vessel approached Kelley’s Island. He then announced that he was a Confederate officer and drew a pistol on the mate. The Philo Parsons was quickly seized without incident.
Fifteen of Johnson Island's three hundred acres were encompassed by a twelve to fourteen-foot high plank fence and used as a place to detain captured Confederate officers. Historian Edward T. Downer notes the Island presented “a frigid and forbidding prospect during the winter months,” especially to “Southern boys who had never seen snow” and “found walking on ice a precarious experience.” Isaac Ridgeway Trimble, the sixty-two year old Major General who lost one of his legs in Pickett’s famous charge at Gettysburg, attempted to relieve the general misery by commanding snowball fights against General Meriwether Jeff Thompson (Missouri).
As 1864 came to a close, there were well over two thousand prisoners behind the fence. They were housed in thirteen two-story barracks (or “block”) that faced each other along a one hundred and fifty-foot street. Although official records indicate only twelve prisoners (of a total of at least twelve thousand) ever escaped from Johnson’s Island, Downer notes the fear or “organized revolts among the prisoners [kept] prison authorities in a constant state of alarm.” Historian Frederick J. Shepard also notes that, almost from the establishment of the prison, there were constant fears of Confederate attacks on the island from Canada.
And, now, at last, John Yates Beall sat, waiting in the water off the miserable Island, watching for a signal, and anticipating his big chance. The signal was to be a flare which would actually be shot from the bow of the Michigan. It would tell Beall and his men that the time was right to attack the ship. Charles Cole, a confederate agent, was the man who was supposed to shoot the flare. He was also in charge of making sure that a gala dinner on board the Michigan that evening would feature drugged champagne. It all may very well have worked had Cole not been arrested in his hotel room earlier that afternoon!
Beall and his crew waited and waited. The longer he waited, the angrier Beall got. And the longer they waited, the more frightened Beall’s men got. The Michigan’s fifteen guns seemed to grow larger and larger with each minute. Eventually, the crew lost hope and encouraged Beall to come back another day. But Beall had never been so close to certain glory and castigated his men for their cowardice and shortsightedness. In an attempt to shame them, he taunted them to sign a written statement which placed all the blame on their shoulders. But the shame Beall was dishing out seemed far less irritating than death or a more long-term visit to Johnson’s Island. So, the signing began. The statement read:
We the undersigned [take] pleasure in expressing our admiration of the gentlemanly bearing, skill and courage of Captain John Y. Beall as a commanding officer and a gentleman, but believing and being well convinced that the enemy is already apprised of our approach, and is so well prepared that we cannot by any possibility make it a success, and having already captured two boats, we respectfully decline to prosecute it any further.There followed seventeen signatures.
Beall asked a friend to send a copy of the trial record to President Lincoln and attached to it a message: "Some of the evidence is true, some false. I am not a spy or guerrilero. The execution of the sentence will be murder."
Dorris notes that a "tremendous effort" was made to have Beall's sentence commuted to life imprisonment." Lincoln gave the case "careful study," but rejected "numerous appeals for clemency" from "men of great personal influence." Pleas came from the Librarian of Congress, the President of the Baltimore and Ohio railroad and numerous lawyers from prominent firms. Six United States Senators formally petitioned Lincoln to exercise clemency along with eighty-five members of the House of Representatives. Carl Sandburg's biography of Lincoln notes "at no time during the four years of the ear had such a mass of formidable influence come forward seeking [a] commutation of death sentence to life imprisonment."
Lincoln biographer William E. Barton sees things from a different angle: Beall was a superior man and a brave man, whose acts, like those of Nathan Hale [bring] deserved applause for their courage, but are clearly liable to the death penalty.
Lincoln did actually grant Beall a six-day reprieve. General Dix was generous in his granting of hanging-attendance passes and several hundred civilians and journalists were on hand when the event finally arrived. On February 25, 1865, Beall stood in front of his last audience, faced himself toward Virginia, and declared a "protest" of his hanging. He called it "a brutal murder."
Forty-five days after Beall's hanging, Abraham Lincoln was assassinated. For many years afterward, more than a few theorists connected Lincoln's death with his refusal to have mercy on John Yates Beall.