When the Lords of the Association, a factious party of the nobility, took up arms against James III, Alexander of Kintail despatched his sons, Kenneth and Hector, with a retinue of 500, to join the Royal standard; but Kenneth, hearing of the death of his father on his arrival at Perth, returned home at the request of the Earl of Huntly; and the clan was led by Hector Roy to the battle of Sauchieburn, near Stirling.
After the defeat of the Royal forces, and the death there in 1488 of the King himself, Hector, who narrowly escaped, returned to Ross-shire and took the stronghold of Redcastle, then held for the rebels by Rose of Kilravock, and placed a garrison in it.
The king, on hearing of the crime, granted Hector a commission of fire and sword against the murderers of his nephews, and gave him a Crown charter to the lands of Gairloch in his own favour dated 1494.
The story of Hector’s dispute with his nephew is recounted both by the Earl of Cromartie and (in the Ardintoul manuscript) by the Reverend John Macrae (died 1704).
It is also supported by Gregory’s History of the Western Highlands and Isles of Scotland, which states that: Hector kept possession of Eilean Donan Castle until compelled by an order from the Privy Council to give it up in 1511 to John, and it appears from the records of the Privy Council that from 1501 to 1508 Hector continued to collect the rents of Kintail without giving any account of them; that he again in 1509 accounted for them for twelve months, and for the two succeeding years for the second time retained them, while he seems to have had undisturbed possession of the stronghold of Eilean Donan throughout.
[9] This view is strengthened by the fact that John obtained a charter under the Great Seal granting him Kintail anew on 25 February 1508-9 – the same year in which Hector received a grant of Brahan and Moy – probably following on an arrangement of their respective rights in those districts; also from the fact that Hector does not appear to have fallen into any disfavour with the Crown on account of his conduct towards John: only two years after Killin raised the action against Hector before the Privy Council, the latter receives a new charter, dated 8 April 1513, under the Great Seal, of Gairloch, Glasletter, and Coirre-nan-Cuilean "in feu and heritage for ever," and he and his nephew appear ever after to have lived on friendly terms.
On 8 September in that year, a grant is recorded to Sir John Dingwall, "Provost of Trinity College, beside Edinburgh, of the ward of the lands of Gairloch, which pertained to the umquhile Achinroy [Hector] Mackenzie.
"[14] Hector Roy was betrothed to a daughter of the Laird of Grant - probably Sir Duncan, who flourished from 1434 to 1485 - but she died before the marriage was solemnised.