Beall and his men attempted a raid on the prison at Johnston Island in September 1864 as they commandeered a ferry boat to transport those who they were attempting to rescue. The raid failed when an informant tipped off Federal authorities.
Not to be denied, Beall decided to instead derail a passenger train carrying other Confederate officers. That plan also failed and he was arrested in Niagara, New York. He was tried, found guilty and sentenced to death.
He had friends, however, in high places. Six U.S. Senators and ninety-one members of Congress signed an appeal to have the conviction overturned, but President Lincoln did not intervene and Beall was hanged on February 24, 1864.
There is a tale about John Wilkes Booth being a friend of John Yates Beall and that he killed Lincoln partly because of his refusal to intervene but this has never been substantiated.
Beall is buried in the Zion Church Cemetery in Charles Town, West Virginia.