The chief responsibility for keeping the Clan Gregor under control belonged to Archibald Campbell, 7th Earl of Argyll. In January 1593 he had been commissioned to enforce the peace among all MacGregors. By March 1594 he was bound under a 20,000-pound surety to keep his men in line. In July 1596, after a payment into the royal treasury, he received an open commission as the King's lieutenant in the bounds of Clan Gregor 'wherever situated.' On 22 April 1601 Allaster MacGregor of Glenstra, chief of Clan Gregor, gave Argyll a bail-bond for the whole clan: any offence by any MacGregor would forfeit clan lands. Yet according to the 19th-century historian William Fraser, Argyll did not use his power to restrain the MacGregors. He used it to set them against Alexander Colquhoun of Luss. The Luss Papers record stolen items in 1594 and through 1600, accumulating evidence of Colquhoun losses.

In 1602 the MacGregor raids grew bolder. Colquhoun of Luss complained to King James VI of Scotland, who - despite a recent Act of Parliament forbidding the carrying of arms - granted Colquhoun and his tenants permission to carry offensive weapons. The MacGregors took the exception as provocation. There were clashes at Glenfinlas. Fraser records that on 21 December 1602, Colquhoun of Luss travelled to Stirling to see the King, accompanied by female relatives of men who had been killed or wounded at Glenfinlas - mothers, wives, and sisters carrying the bloodied shirts of their dead. The King was moved. He vowed vengeance and granted Colquhoun a commission of lieutenancy with powers to repress the MacGregors and apprehend the perpetrators. The Colquhouns rode out to enforce that commission. The MacGregors raised a force to meet them.

On 7 February 1603, Allaster MacGregor led his division in a furious charge against Alexander Colquhoun of Luss and his men. The Colquhouns held the line for a time. Tactical disadvantage broke them - they were forced into boggy ground at the farm of Auchengaich, where they fell into disorder. The MacGregors pressed the attack. When the Colquhouns retreated, they had to fight through John MacGregor's division, and that second engagement proved even more disastrous. Alexander Colquhoun was chased the whole way back to Rossdhu Castle on the western shore of Loch Lomond, which gave him refuge. Fraser puts the Colquhoun dead at 140. Many more were wounded. The MacGregors lost few men; one of them was John MacGregor, the chief's brother. A grey stone in the glen is said to mark his grave.

There is a story - John Parker Lawson recorded it - that a group of theological students had come to watch the battle, or perhaps were on an excursion nearby. The chief of the Colquhouns is said to have put them in a barn for safety. After the battle they fell into MacGregor hands, and were placed under the care of a cadet named Dugald Ciar Mhor, direct ancestor of Rob Roy MacGregor. Dugald is said to have killed them all. When his chief asked where the youths were, he answered: 'Ask that, and God save me.' The tale was traditional. Lawson, after weighing it, concluded it was probably not true. No reference to the massacre appears in the indictment against the MacGregors who fought at Glen Fruin - and the Crown prosecutors brought every charge they could. Lawson thought it impossible that such an atrocity would have escaped them. Walter Scott alluded to the story in the introduction to his novel Rob Roy, blaming Clan MacFarlane allies instead.

What happened next was unprecedented in Scottish royal policy. King James VI - already on the verge of inheriting the English throne as James I - sought to make the Highlands and Islands 'answerable to God, justice and himself' and to fold them into his new Britain. One radical expression of this was the systematic destruction of the MacGregors. Allaster MacGregor, the chief who had led the charge at Glen Fruin, was executed in 1604 along with eleven of his chieftains. In 1633 it became legal under Scottish law to kill MacGregors on sight and to hunt them with bloodhounds. Bearing the surname MacGregor was itself outlawed. The clan persisted - quietly, under assumed names, scattered - for the next century and a half. Rob Roy MacGregor would emerge as a folk hero from this dispossessed community a century later. The Colquhouns kept their name and their lands but had buried a generation in the glen.

In July 1967 archaeologists excavated a mound in Glen Fruin that local tradition identified as the burial place of the Colquhoun dead. They found a Bronze Age encampment instead, not 17th-century war graves. The bodies of the men who died in 1603 were buried elsewhere, in ground long since lost to memory. Glen Fruin today is quiet pasture, threaded by a road and a stream, opening toward Loch Lomond. Walter Scott's introduction to Rob Roy, the poem Dora Marcelli, The Last of Her Race by David Wardlaw Scott, and the ballad The Raid of Glen Fruin by Peter McArthur all keep the memory alive. So does the song The Bloody Sarks - the bloodied shirts that women carried to Stirling, asking the King for justice and triggering the chain of events that ended a clan.