Hector's leadership was not universally acknowledged by the clan and as a result the Earl of Moray who was also a relation of William had him and his mother removed to his own house.
Subsequently, a royal mandate was issued on 9 November 1528 for the extermination of the invading Clan Chattan, during the reign of James V of Scotland.
It was addressed to the sheriffs of Kincardine, Aberdeen, Banff, Elgin, Forres, Nairn and Inverness and to the Earl of Moray himself, who was lieutenant general of the north.
[1] According to 19th historian Alexander Mackintosh-Shaw, if this mandate had been acted upon by all of the persons to whom it was addressed, then the history of the Clan Chattan would have probably been ended.
Two years later the Earl of Moray marched into Mackintosh country and took 300 prisoners, many of whom were executed including Hector's brother, also called William.
He goes onto say that Lachlan Mackintosh who was the son of the man who had murdered William's father, Lachlan Beg Mackintosh, 14th chief, had been sowing the seeds of discontent among the Clan Macpherson who were part of the Clan Chattan and that he was no well-wisher of William.
Huntly then seized chief William Mackintosh and put him on trial on 2 August 1550 at Aberdeen.
[1][3] In 1554, Huntly, along with the Earl of Argyll were ordered to exterminate the Clan Macdonald of Clanranald, but both failed in their objectives; Huntly, because the Highlanders were so much exasperated against him for having executed William Mackintosh in 1550, that he declined to face Clan Ranald with such an army, disbanding his forces.