Fordun says that James displayed marks of great joy as these turbulent and haughty spirits, caught in the toils which he had prepared for them, came voluntarily within reach of his regal power, and that be "caused to be arrested Alexander of the Isles, and his mother, Countess of Ross, daughter and heiress of Sir Walter Lesley, as well as the more notable men of the north, each of whom he wisely invited singly to the Castle, and caused to be put in strict confinement apart. There he also arrested Angus Duff (Angus Dubh Mackay) with his four sons, the leader of 4000 men from Strathnarven (Strathnaver.) Kenneth More, with his son-in-law, leader of two thousand men; [All writers on the Clan Mackenzie have hitherto claimed this Kenneth More as their Chief, and argued from the above that Mackenzie had a following of two thousand fighting men in 1427. It will be seen that Alexander was Chief at this time, but Kenneth More may have been intended for MacKenneth More, or the Great Mackenzie. He certainly could have had no such following of his own name.] John Ross, William Lesley, Angus de Moravia, and Macmaken, leaders of two thousand men; and also other lawless caterans and great captains in proportion, to the number of about fifty Alexander Makgorrie (MacGodfrey) of Garmoran, and John Macarthur (of the family of Campbell), a great chief among his own clan, and the leader of a thousand and more, were convicted, and being adjudged to death were beheaded. Then James Cambel was hanged, being accused and convicted of the slaughter of John of the Isles (John Mor, first of the Macdonalds of Isla.) The rest were sent here and there to the different castles of the noblemen throughout the kingdom, and were afterwards condemned to different kinds of death, and some were set at liberty." Among the latter was Alexander of Kintail. The King sent him, then a mere youth, to the High School at Perth, at that time the principal literary seminary in the kingdom, while the city itself was frequently the seat of the Court.
During Kintail's absence it appears that his three bastard uncles ravaged the district of Kinlochewe, for we find them insulting and troubling "Mackenzie's tenants in Kenlochewe and Kintail Macaulay, who was still Constable in Ellandonnan, not thinking it proper to leave his post, proposed Finlay Dubh Mac Gillechriost as the fittest person to be sent to St. Johnston, now Perth, and by general consent he accordingly went to inform his young master, who was then there with the rest of the King's ward children at school, of his lordship's tenants being imposed on as above, which, with Finlay's remonstrance on the subject, prevailed on Alexander, his young master, to come home, and being backed with all the assistance Finlay could command, soon brought his three bastard uncles to condign punishment." [Genealogical Account of the Macraes.]
The writer of the Ardintoul MS. says that Finlay "prevailed on him to go home without letting the master of the school know of it. Trysting with him at a certaiu place and set hour they set off, and, lest any should surprise them, they declined the common road and went to Macdougall of Lorn, he being acquainted with him at St. Johnston. Macdougall entertained him kindly, and kept him with him for several days. He at that time made his acquaintance with Macdougall's daughter, whom afterwards he married, and from thence came to his own Kintail, and having his authority and right backed with the power of the people, he calls his bastard uncles before him, and removes their quarters from Kenlochewe, and gave them possessions in Glenelchaig in Kintail prescribing measures and rule for them how to behave, assuring them, though he pardoned them at that time, they should forfeit favours and be severely punished if they transgressed for the future; but after this, going to the county of Ross to their old dwelling at Kenlochewe, they turned to practice their old tricks and broke loose, so that he was forced to correct their insolency and make them shorter by the heads, and thus the people were quit of their trouble."
The young Lord of the Isles was at the same time that Mackenzie went to Perth sent to Edinburgh, from which he soon afterwards escaped to the North, at the instigation of his mother, the Countess, raised his vassals, and, joined by all the outlaws and vagabonds in the country, numbering a formidable body of about ten thousand, he laid waste the country, plundered and devastated the crown lands, against which his vengeance was specially directed, razed the Royal burgh of Inverness to the ground, pillaged and burned the houses, and perpetrated every description of cruelty. He then besieged the Castle, but without success, after which he retired precipitately towards Lochaber, where he was met by the Royal forces, commanded by the King in person. The Lord of the Isles prepared for battle, but he had the mortification to notice the desertion of Clan Chattan and Clan Cameron, who had previously joined him, and of seeing them going over in a body to the Royal standard. The King immediately attacked the island chief and completely routed his forces, while their leader sought safety in flight. He was vigorously pursued, and finding escape or concealment equally impossible, and being reduced to the utmost distress, hunted from place to place by his vigilant pursuers, the haughty chief resolved to throw himself entirely on the mercy of His Majesty, and finding his way to Edinburgh in the most secret manner, and on the occasion of a solemn festival on Easter Sunday, in 1429, at Holyrood, he suddenly appeared in his shirt and drawers before the King and Queen, surrounded by all the nobles of the Court, while they were engaged in their devotions before the High Altar, and implored, on his knees, with a naked sword held by the point in his hand, the forgiveness of his sovereign. With bonnet in hand, his legs and arms quite bare, his body covered only with a plaid, and in token of absolute submission, he offered his sword to the King. His appearance, strengthened by the solicitations of the affected Queen and all the nobles, made such an impression on His Majesty that he submitted to the promptings of his heart against the wiser and more prudent dictates of his judgment. He accepted the sword offered him, and spared the life of his captive, but immediately committed him to Tantallon Castle, under the charge of William Douglas, Earl of Angus. The spirit of Alexander's followers, however, could not brook this mortal offence, and the whole strength of the clan was promptly mustered under his cousin Donald Balloch, who led them to Lochaber, where they met the King's forces under the Earls of Mar and Caithness, killed the latter, gained a complete victory over the Royal army, and returned to the Isles in triumph, with an immense quantity of spoil.
James soon after proceeded north in person as far as Dunstaffnage; Donald Balloch fled to Ireland; and, after several encounters with the rebels, the King obtained the submission of the majority of the chiefs who were engaged in the rebellion, while others were promptly apprehended and executed to the number of about three hundred. The King thereupon released the Lord of the Isles from Tantallon Castle, and granted him a free pardon for all his rebellious acts, confirmed him in all his titles and possessions, and further conferred upon him, in addition, the Lordship of Lochaber, which had previously, on its forfeiture, been granted to the Earl of Mar. After his first escape from Edinburgh, the Lord of the Isles again in 1429 raised the standard of revolt. He for the second time burnt the town of Inverness, while Mackenzie was "attending to his duties at Court."
Kintail was recalled by his followers, who armed for the King, and led by their young chief on his return home, they materially aided in the overthrow of Alexander of the Isles at the same time securing peace and good government in their own district, and among most of the surrounding tribes. Alexander is also found actively supporting the King, and with the Royal army, during the turbulent rule of John, successor to Alexander, Lord of the Isles, who afterwards, in 1447, died at peace with his sovereign.
James I. died in 1460, and was succeeded by James II. When, in 1462, the Earl of Douglas, the Lord of the Isles, and Donald Balloch of Isla entered into a treaty with the King of England for the subjugation of Scotland, on condition, in the event of success, that the whole of Scotland, north of the Firth of Forth, should be divided between them, Alexander Mackenzie stood firm in the interest of the ruling monarch, and with such success that nothing came of this extraordinary compact. We soon after find him rewarded by a charter in his favour, dated 7th January 1463, confirming him in his lands of Kintail, with a further grant of the "5 merk lands of Killin, the lands of Garve, and the 2 merk lands of Coryvulzie, with the three merk lands of Kinlochluichart, and 2 merk lands of Ach-na-Clerich, the 2 merk lands of Garbat, the merk lands of Delintan, and the 4 merk lands of Tarvie, all lying within the shire and Earldom of Ross, to be holden of the said John and his successors, Earls of Ross." This is the first Crown charter in favour of the Mackenzie chief of which any authentic record exists.
Alexander continued to use his great influence at Court, as well as with John Lord of the Isles, for the purpose of bringing about a reconciliation between his Majesty and his powerful subject during the unnatural rebellion of Angus Og against his father. The King, however, proved inexorable, and refused to treat with the Earl on any condition other than the absolute and unconditional surrender of the earldom of Ross to the Crown, of which, however, he would be allowed to hold all his other possessions in future. These conditions the island chief haughtily refused, again flew to arms, and in 1476 invaded Moray, but finding that he could offer no effectual resistance to the powerful forces sent against him by the King, he, by the seasonable grants of the lands of Knapdale and Kintyre, secured the influence of Colin, first Earl of Argyll, in his favour, and with the additional assistance of Kintail, procured remission of his past offences on the conditions previously offered to him and resigning for ever, in 1476, the Earldom of Ross to the King, he "was infeft of new" in the Lordship of the Isles and the other possessions which he had not been called upon to renounce. The Earldom was in the same year, in the 9th Parliament of James III., irrevocably annexed to the Crown, where the title and the honours still remain, held by the Prince of Wales.