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The MacIains were constantly involved in trouble with the law and with neighbouring clans for their consistent raiding, pillaging and cattle rustling. The clan had particular trouble with neighbouring Campbell clans.

There were many Highland clans at the time who were a possible threat to the new regime in London under King William of Orange, and many who openly swore their allegiance to the deposed Stuart King - James VII. King William himself was more concerned with his war against the French King, Louis XIV. Problems in the Highlands were little more than a nuisance to him.

The order came through that the chiefs were to sign an oath of allegiance to King William by January 1, 1692. Although this oath was originally packaged with the promise of money and land for the clans, by the time it was circulated publicly the terms were much more threatening - the clans would sign the agreement or be punished with the "utmost extremity of the law". The man who used this deadline to his own political ends was the Secretary of State, John Dalrymple, Master of Stair, who was a Lowlander and a Protestant. He disliked the Highlanders and viewed their whole way of life as a hindrance to Scotland, which would be better served, he thought, in union with England. He had a particular dislike for the MacDonalds of Glen Coe.

Another problem for the clans at the time was the fact that many of them were bound by an oath to James Stuart, the deposed King in France. It was December 12 before James had released the clans from their oath and December 28 before a messenger arrived in the Highlands with the news - leaving only three days until the deadline.

As the worst of winter swept through Glen Coe on December 31, MacIain, fearful for the safety of his clan, left for Fort William to sign the oath. From here he was turned back by Colonel John Hill, who explained that the oath had to be taken before a sheriff. This involved a 60 mile trek to Inveraray: the principle town of his enemies, the Campbells. Still MacIain could have met the deadline had he not been captured by Campbell soldiers serving in Argyll’s regiment. They detained him for a day, whilst he was detained for several more days in Inveraray due to the absence of the Sheriff, Sir Colin Campbell. Even then, MacIain had to plead with the Sheriff to accept the late oath.

In Edinburgh, the Master of Stair with his legal team declined the late-delivered oath. Everything was ready for the fall which Stair had engineered for the clan. The orders were explicit: the MacDonalds were to be slaughtered - "cut off root and branch". Three commanders were to be involved - two from the Campbell-dominated Argyll regiment and one from Fort William. In the end, two of those never arrived in time, claiming delay through bad weather. It was Captain Robert Campbell of Glenlyon, a desperate man who lost his all through gambling, who carried out Stair’s final order: "to put all to the sword under seventy".

The soldiers arrived at Glen Coe 12 days before the massacre, as friends, seeking shelter due to the fact that the fort was full. The MacDonalds, honouring the Highland hospitality code, duly gave the soldiers quarter in their own houses. For 12 days they lived together with neither the clan nor the common Argyll soldiers knowing what lay ahead.

On the night of February 13 a blizzard howled through Glen Coe, giving whiteout conditions. As the clan slept the house guests gathered, received their orders, and set about systematically killing everyone they could. 38 lay dead the next morning, including the chief, MacIain. Many more escaped into the hills, some finding shelter before the elements could kill them, some, including MacIain’s elderly wife, dying on the mountainside.

It seems certain that some of the Campbell soldiers, disgusted with their orders, alerted the families who had been their hosts, giving them time to escape and at least wrap up against blizzard. Many historians also claim that the lateness of the other two companies of soldiers who were to help in the slaughter was deliberate - a ploy not to be involved in such an atrocity.

The nation of Scotland, although used to war and murder in its many forms, was outraged by the callousness of the massacre of Glen Coe. For the Jacobites in Edinburgh it was a powerful piece of anti-government propaganda. An inquiry was held and Scottish Parliament declared the whole affair an act of murder. John Dalrymple, the Master of Stair, resigned and the matter was forgotten by the government. In Scotland it passed into legend. The Campbells were accursed in much of the Highlands and even to this day the old Clachaig Inn at Glen Coe carries the sign on its door, 'No Campbells'.