On 30 March 1866 Stephenson was the lieutenant-in-command of HMS Heron, serving in North America and the West Indies, and becoming the commanding officer of a gun-boat on the Canadian lakes during the Fenian raids of 1866.
He served in the local militia, reaching the rank of colonel, and served during the Fenian raids.
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He did not take any part personally in the attempted insurrection in Ireland or in the raids on Canada, although his advice counted for much in these enterprises.
In 1865, through a companion in arms named John O'Neill, he was brought into contact with Fenianism, and having learnt of the Fenian plot against Canada (the Fenian raids), he mentioned the designs when writing home to his father in England.
His son Joseph Kirby (1844–1937) enlisted as mercenary in the 184th Regiment of New York State Infantry of the Union Army during the American Civil War and returned to Canada in 1865 and joined the Ashberminam Company of Volunteers during the Fenian Raids of 1866.