In his negotiations with Russell, during a truce in the
Nine Years War, Hugh O'Neill included terms for the treatment of O'Byrne, and reinforced his point with the capture of the Blackwater fort, which was said to have been in response to the lord deputy's campaign in Wicklow. O'Byrne sought pardon for himself and his family – excluding his most wayward sons – in the summer of 1596, by which time he was old and sick. He presented himself on his knees to the council sitting at Dublin to seek mercy and was granted his pardon upon petition to the queen. Even so, he was in alliance with O'Neill, acting as a Leinster base for rebel influence and maintaining a force on the borders of the Pale. The fort at Ballinacor was retaken by O'Byrne, and the attacks on government forces in Wicklow began again. He had also allied with the O'Mores, Kavanaghs, O'Connors and O'Tooles, and was thought by Russell to be of far greater ability than O'Neill. However, the rest of the O'Byrnes were not considered a threat, indeed the clan were divided, with some engaging in the hunting down of Fiach, and a new fort was built at Rathdown. During the winter, Russell scoured the mountains, taking in cattle and heads. He crossed the bridge at Ballinacor ford against resistance on 24 September 1596 and stayed on the mountain with his cavalry. Meanwhile, Captain Lee was sent with a force to Fananerin, on the west side of Glenmalure (i.e. in Manning's bog north of Greenane north of the river), where he burned the town before returning to camp. O'Neill complained of the attacks on O'Byrne, and Lee was left to engage in sporadic fighting. The government believed that O'Neill was attempting to divert the attacks, and so Russell made the final push in March 1597, when he marched over the mountains to Fananerin and on to Ballinacor and into the glen. There he made a show of dining, and knighted an officer in the place where one of the
Carews had been slain during Grey's campaign in 1580. Russell withdrew, only to return two months later on the information of the northern branch of the O'Byrne clan. He was due for recall to London, and it seems that the defeat of O'Byrne himself had become the ultimate aim of his government. Again the Lord Deputy came to Fananerin (Sunday, 8 May 1597), with troops converging on the town from three directions. O'Byrne was in the company of a few swordsmen, who were killed at the first incursion, and fled on foot. He was compelled by exhaustion to seek refuge in a cave, where Captain
Thomas Lee caught up with him. He was executed by Lee's soldiers, and his own sword was used to cut off his head, which was presented to Russell before his return to Dublin the next day. It was the governor's final success in Ireland. Lee later met with O'Byrne's son, Phelim, at
Rathmines, and swore the killing had not been of his choice. ==Lost head==