John Allen was a Protestant native of Dublin, where he was for some time a partner in a drapery business. He joined the Society of United Irishmen in the city and became involved in a broader conspiracy to coordinate an Irish insurrection with a French landing in the British Isles and a rising by Jacobin radicals in England.
Along with Father James Coigly, Arthur O'Connor, Benjamin Binns (of the London Corresponding Society) and Jeremiah Leary, he was tried for high treason at Maidstone in February 1798. The party had been arrested while attempting to make a Channel crossing to France. In Coigly's coat pocket had been found what proved to be the only admissible evidence of treason, an address from "The Secret Committee of England’" to the Directory of France. While its suggestion of a mass movement in England primed to welcome Napoleon, the "hero of Italy", was scarcely credible, it was proof of intent to invite and encourage a French invasion. Coigly refused the offer of his life in return for implicating Allen and his fellow defendants who were acquitted.[1]
Following the suppression of the United Irish insurrection in the summer of 1798, Allen joined Robert Emmet in seeking to re-establish the republican organisation on strictly military lines. In 1800 he is said to have accompanied Emmet on a mission to Irish exiles in Cadiz.[2]
In July 1803, an accidental explosion at one of their arms depots in Dublin forced them to declare themselves and attempt a seizure of the city. Allen led a rebel band, according to one witness of 300, but they failed to effect a conjunction with the command of Emmet and Myles Byrne in Thomas Street.[3] Unaware of Allen's approach, Emmet ordered his men to disband, and the attempt to seize the city broke up in series of disorderly altercations.
Allen is said to have escaped Dublin in the uniform of the Trinity College Yeomanry corps, and to have been "put into a cask, carried to George's Quay and shipped for France".[2]