In March 1689,
James VII of Scotland landed in Ireland in an attempt to regain his throne from
William II, and
John Graham of 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.
Despite this, the continuing need to police the Highlands used resources William needed for the
Nine Years' War. A peaceful Scotland was especially 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.