The Jacobite rising of 1689 had been largely suppressed by May 1690, but policing the Highlands continued to divert military resources from the Nine Years' War in Flanders. In late 1690, clan leaders loyal to the exiled House of Stuart agreed to swear allegiance to William and Mary in return for a cash payment of twelve thousand pounds. Disagreements over dividing the money meant that by December 1691, none of the clans had taken the oath. Lord Stair, the Secretary of State for Scotland, decided to make an example. While other chiefs also missed the deadline, the Glencoe MacDonalds were selected through a combination of clan politics and their reputation for lawlessness. MacIain, the aging chief, had set out on 30 December to swear his oath at Fort William, only to be told the garrison commander was not authorized to administer it. Redirected to the magistrate at Inveraray, he finally swore on 6 January 1692 -- six days late. Stair, who had openly called for the extermination of the clan, had his pretext.

On 1 February 1692, two companies of soldiers -- around 120 men under Captain Robert Campbell of Glenlyon -- arrived in the glen and were billeted among the MacDonald households. Under the ancient Highland tradition of hospitality, the MacDonalds fed and sheltered them for twelve days. Campbell's orders, signed by Major Robert Duncanson, were explicit: every MacDonald under seventy was to be put to the sword, and the killing was to begin at five in the morning so that 'none of the said rebels escape.' The operation was meant to be a coordinated slaughter, with troops blocking both exits of the narrow glen. But the blocking forces under Lieutenant Colonel James Hamilton arrived hours late, and the killing, though devastating, was not the total annihilation that Stair had demanded. Approximately thirty men were killed in the initial assault, including MacIain and several of his family. An unknown number of women and children died of exposure after fleeing into the snow-covered mountains with their homes burning behind them.

The massacre shocked Scotland in ways that previous clan violence had not. This was not a battle or a cattle raid -- it was the deliberate violation of guest-right, the ancient code that made a host responsible for the safety of those sheltered under his roof. The soldiers had eaten MacDonald food, slept in MacDonald homes, and played cards with MacDonald families before turning their weapons on them. A parliamentary inquiry in 1695 concluded that the massacre constituted 'murder under trust,' one of the most serious charges in Scots law. Stair was found to have exceeded his instructions and was temporarily removed from office. King William, whose orders had authorized 'fire and sword' against those who missed the oath deadline, escaped formal censure but suffered lasting damage to his reputation in Scotland. The massacre became a powerful engine of Jacobite sentiment in the Highlands. When Charles Edward Stuart raised his standard at Glenfinnan in 1745, the memory of Glencoe was among the grievances that brought clansmen to his cause. Three centuries later, the Clachaig Inn at the foot of the glen still displays a sign reading 'No hawkers or Campbells.' It is a joke, mostly.