He was fostered in the households of the O'Cahan's, the O'Cuinn's and possibly MacDonnell Gallowglass, due to the danger posed by other O'Neill family members.
Collectively the brothers were known as the "MacShanes", and waged a continual war from 1583 to 1591 for domination of Ulster with the backing of a Scottish army made up of Macleans and MacDonnells.
Henry and Con made a push for power in the summer of 1584; their actions precipitated the temporary collapse of the authority of Turlough Luineach O'Neill.
Henry was unable to quickly retaliate, as he and his brother Art were imprisoned in Dublin Castle in 1585 by Lord Deputy Sir John Perrot, who was on a tour of the north that year.
Art died from exposure, having suffered more for his advanced age compared to his companions during his imprisonment, and after having a rock dropped on him during their flight from the castle, in Glenmalure, during the escapers' desperate trek towards the land of Fiach McHugh O'Byrne, and Perrot enabled Hugh O'Neill and Turlough Luineach to attack the territory of James O'Donnelly, the main supporter of the MacShanes.