Following the suppression of the First Jacobite Uprising, King William offered pardons to Jacobite clan chiefs, provided they swore allegiance to him by December 31, 1691. Although the MacDonalds of Glen Coe intended to do so, they delayed leaving until the 30th. They went wrongly to Inverlochy (now Fort William) and were further delayed by the weather. As a result they arrived late and took the oath five days after the deadline. William decided to make an example of the clan. He enlisted the Campbells, longtime enemies of the Macdonald to do so and the Massacre at Glen Coe was the result.
The massacre had roots in the Campbell-MacDonald feud, which dated back to 1500. The Campbells were prosperous and ambitious - with friends in high places. The MacDonalds were notorious, particularly for their ability to make cattle "disappear."
In 1501 the Glen Coe MacDonalds (with others) captured the Campbell fortress on Loch Awe, rescuing Donald Dhu - the last Lord of the Isles. Donald Dhu had been imprisoned for more than 40 years by his Campbell grandfather.
For years skirmishes and raids took place around Glen Lyon. In the early years of the conflict 36 Glen Coe MacDonalds were hanged by Mad Colin Campbell of Glen Lyon. In 1646 the MacDonalds attacked the Campbells after a wedding, killing 36. In 1685, when the Campbells' power was at low ebb (two Earls of Argyll had been executed), the MacDonalds pillaged Campbell land and effectively ruined many families. Scottish leaders often took advantage of the longstanding feud as well. The Campbells fought with Cromwell and the MacDonalds fought with Montrose during the Civil War.
At the time of the massacre, the MacDonald clan consisted of several hundred people in an area of approximately 10 miles. The clan was led by Alastair, 12th chief. He had fought with Bonnie Dundee and had a long career of raiding. He had been imprisoned in Inverary for either committing or allowing the murder of one of his clan, but escaped. He was well over six feet and had long white hair with a spiked mustache. Intensely popular with his clan, he was not as well regarded by many in the Highlands.
The massacre was led by Captain Robert Campbell, the great-grandson of Mad Colin and one of those families who had been damaged by MacDonald raids in 1685. He was 60 and his niece was married to Alastair's son. He was an alcoholic and gambler who had lost much of what remained of his estate due to incompetence and vice. Despite these facts, he may not have been aware of his mission when he first went to the MacDonalds.
Campbell arrived at Glen Coe and asked quarters for two companies (approximately 120 men). They were housed and fed for ten days before Campbell received written orders from Major Robert Duncanson. They were ordered specifically to "root out the old fox and his cubs" and to put everyone under 70 "to the sword."
On February 13, 1692, the massacre took place as planned in various parts of Glen Coe. At Inverrigan, Invercoe, Carnoch, Achnacon and Achtriochtan, members of the MacDonald clan were killed. In all perhaps 30 were killed and 300 fled to the hills. Many died of cold and starvation. Incredibly two of the chief's sons and a grandson escaped.
Within two weeks news of the massacre was out and a pamphlet by Charles Lesley, an Irishman, turned the event into national scandal. It was particularly abhorrent to Highlanders, because it violated their strict code of hospitality and because of the government's complicity in its genocidal intent. In spite of the outrage, there were no long term repercussions for the perpetrators.
However, John, the 13th MacDonald Chief was given a pardon and rebuilt his home. Ironically John's brother, Alastair fought in 1715 alongside John Campbell, who had led the massacre. As a result, both had their estates confiscated.
This information is from various sources, primarily from the National Trust for Scotland's Glen Coe publication.