Before the Civil War, Boyle had headed the National Rifles, a pro-Southern militia unit.  When war did break out, he set aside his professional practice and offered his services to the state of Virginia, becoming a Major in the Confederate Army. Post commander at Gordonsville, this critical location allowed for him to pass messages quickly to and from the Headquarters of the Army of Northern Virginia, and he quickly became an important Confederate agent.  Boyle was part of numerous undercover operations and communications during the Civil War. It has even been suggested that he could have been aware of or played a small role in both Thomas R. Harney's attempt to bomb the White House and John Wilkes Booth's assassination of President Abraham Lincoln.  After the war, Boyle's vast properties were seized by the government, and he planned to move and settle in Mexico, though this was never realized.  

At least four of the signatories to the petition directed to President Johnson (see below) attended President Lincoln at Ford's Theatre or the Petersen House after he was shot by John Wilkes Booth: Albert F. King, Charles H. L. Liebermann, Charles M. Ford,, and Jame C. Hall. Other notable petioners include Dr. Alexander Y. P. Garnett, physician to Jefferson Davis and Robert E. Lee. Biographical notices of many of the signers can be found in History of the Medical Society of the District of Columbia (Washington, D.C., 1909).