In March 1689, James II of England and VII of Scotland[c] landed in Ireland in an attempt to regain his throne and John Graham, Viscount Dundee recruited a small force of Highlanders for a similar campaign in Scotland. Despite victory at the Battle of Killiecrankie on 27 July, Dundee was killed and organised Jacobite military resistance ended with defeats at the Battle of Dunkeld in August 1689 and Cromdale in May 1690.
The continuing need to police the Highlands used resources William needed for the Nine Years' War. A peaceful Scotland was important since links between Irish and Scottish branches of the MacDonalds as well as Scottish and Ulster Presbyterians meant unrest in one country often spilt into the other.
The Glencoe MacDonalds were one of three Lochaber clans with a reputation for lawlessness, the others being the MacGregors and the Keppoch MacDonalds. Levies from these clans served in the Independent Companies used to suppress the Conventicles in 1678–80 and took part in the devastating Atholl raid that followed Argyll's rising in 1685. They also combined against their Maclean landlords in the August 1688 battle of Maol Ruadh, putting them in the unusual position of being considered outlaws by both the previous Jacobite administration and the new Williamite one.