The Episcopalian James VI was at odds with Presbyterianism that saw little difference between Episcopal Bishops and Catholic Bishops. James VI, and Charles I after him, both declared themselves head of church and state, but were gradually losing control of both. In 1638 the National Covenant was signed by the Protestants of Scotland. It amounted to a declaration of war on Catholicism and Episcopalian Protestants that included most of Clan Donald.
In 1640 The Earl of Argyll was given a commission “of fire and sword to pursue not only proven enemies to religion, but also unnatural to their country to the utter subduing and rooting them out”. Glengarry was one of the first clans to fall victim of the Covenanters. The Covenanters led 4,000 men into Glengarry to burn chapels and kill men, women, and children who believed in the church being governed by Bishops. In 1643 the Earl of Antrim entered into an agreement with the Earl of Montrose to raise an army to fight against Argyll and the Covenanters. Angus of Glengarry joined his kinsmen of Antrim and Sleat to fight for Montrose. According to British histories the “Earl of Montrose raised an army of Irish and Highlanders” in 1643 to fight for the King against the Covenanters. Almost half of Montrose’s army was made up of 1,500 Clan Donald including 500 of Glengarry. They were victorious against Argyll’s Covenanters. The Keppoch bard, Iain Lom (Gaelic thin) described the battle of Inverlochy urging the Campbells to “not forget their bonnets floating in the Lochy”, and advised them to “take swimming lessons before returning to Glengarry”.
According to British Histories the Irish and Highlanders deserted Montrose at Philiphaugh, but the truth is Clan Donald supported Montrose only to regain the old Lordship of the Isles and oppose those who took over the Lordship. The Antrim McDonnells attacked the Campbells in Kintyre to recover the lands once held by their clan under Iain Mhoir. Glengarry returned to Invergarry castle after re-establishing their right to live on their lands “by sword”. Without Clan Donald Montrose suffered a total defeat at Philphaugh and fled to shelter at Invergarry. If Montrose had felt deserted by Clan Donald, as British history claims, why would he take shelter among those who “deserted” him?
In 1649 Cromwell had King Charles I executed. This was an unthinkable act both in England and Scotland. Charles II was in Holland when he was declared King of Scotland. In 1661 Angus of Glengarry was raised “to the peerage” under the name “Lord Macdonell and Aros”. The Glengarry branch have spelled their name Macdonell since (stating it more closely reflects the Gaelic pronunciation). The odd turn of events that led up to the loss of the Highland way of life hinged on poor timing. When Glengarry finally gave allegiance to the King, all Scotland and England turned against him. That fierce loyalty was again displayed in 1745 when Bonnie Prince Charlie landed in Clan Donald lands to raise his Highland army and regain his throne. After the tragic defeat of the Highlanders at Culloden, Bonnie Prince Charlie took refuge at Invergarry before fleeing to the Isle of Skye. Like Manannan mac Lir of Celtic mythology, Glengarry found itself a victim of changing religion.