Although shot in the jaw at the Battle of Carnifex Ferry in Western Virginia, 10 September 1861, he volunteered to return to duty before the end of the year.

[6] Kelly was commissioned in January 1862, and later seconded to the staff of Major General George Henry Thomas (later "The Rock of Chickamauga") of the XIV Corps, United States Army of the Cumberland, as a Signal Officer.

General Thomas's need for Kelly's services was trumped by a new Army regulation requiring that all officers of the Signal Corps have university degrees by the following February.

[9] After the end of the war, Kelly learned about the establishment of the Irish Republican Brotherhood (IRB) and joined the movement in New York.

Kelly's authority continued to grow when, on 24 November 1865, he was able to arrange the rescue of IRB President James Stephens from Richmond Prison in Dublin.

[3] In September 1865, the Dublin Castle administration suppressed publication of The Irish People, a Fenian run newspaper and its staff.

The first, proposed by John Devoy, would see the IRB attempt to capture important military targets in and around Dublin City using local recruits and deserters from the British Armed Forces.

As Halpin had outranked Kelly in the Union Army, his plan gained traction within the IRB without necessarily receiving an official endorsement.

[3] On 11 February 1867 Kelly ordered a raid on Chester Castle in England, with the objective of securing arms for the rebellion, this action had to be aborted.

The rising failed as a result of lack of arms and planning, but also because of the British authorities' effective use of informers, as most of the Fenian leadership had been arrested before the rebellion took place.

In response, the IRB met in secret in August in Manchester and considered forming a new supreme council which would continue to act as a "Provisional Government-in-exile".

Although the Provisional government idea was not truly acted upon, Kelly was formally recognised as the President of the IRB and successor of James Stephens.

[12] Seven days later, Kelly and Deasy were being transferred from the courthouse to the county jail on Hyde Road, Manchester, when about thirty supporters attempted to free them.

After his death, the New York State Senate posthumously awarded him a Liberty Medal, its highest honour, in recognition of his past work for the US armed services.

[15] He and his second wife, Anna Frances (née Dunne) (May 1860 – September 1913) are buried in Woodlawn Cemetery in the Bronx, New York City.