In 1863, Fennell became one of the first Fenians recruited from County Clare; he then helped recruit and organize a group of men in preparation for the Fenian Rising. On 5 March 1867, six Fenians men entered the Kilbahacoastguard station, and demanded the station's arms "in the name of the Irish Republic". A scuffle ensued, and Fennell was shot through the hip and testicle. The group retreated, and Fennell was treated for his injuries. He was arrested three days later. Tried for treason in the Clare Assizes, on 15 July 1867 he was found guilty and sentenced to ten years' penal labour. Initially he was lodged at Mountjoy Prison, a clearinghouse for political prisoners; later he was transferred to Portland prison.
Fennell remained in the Western Australianpenal system until March 1871, when he received a conditional pardon under a Royal Clemency announced by William Ewart Gladstone the previous December. Banned from returning to the United Kingdom, Fennell sailed for New Zealand in May 1871. On arrival, he was immediately arrested and deported to New South Wales, as New Zealand had laws restricting immigration of ex-convicts. New South Wales had similar laws, but did not arrest him, presumably because he made known his intention of emigrating to the United States. He sailed for San Franciscoon board the City of Melbourne. In 1872 he went to Connecticut. While there, he was approached by John Devoy about plans to rescue the military Fenians still in Western Australia's penal system. Fennell's suggestion was ultimately implemented in the Catalpa rescue. Although Devoy and the other Irish-Americans always credited Fennell with the original idea, Fennell himself claimed that the idea came from "two gentlemen in Australia whose names it would not be well to mention, and a Rev'd gentleman now out west in this country". In 1874 Fennell married Margaret Collins, and they moved to Elmira, New York. Fennell set up as the operator of the Commercial Hotel, and also served as the local agent for the Cunard Line, a city park commissioner, and Elmira's first Superintendent of Public Works. He helped to raise funds for various Irish causes, such as the Kilrushmonument to the Manchester Martyrs. Fennell's first son, Thomas Francis Fennell was the head football coach at Penn State from 1904 to 1908.
Death
Fennell died on 23 February 1914 after a brief illness. He was survived by his wife and three children.