In the meantime, James did not remain long at the French court. With a small force of French troops he sailed for Ireland, the most Catholic part of the realm. Once there he asserted his hereditary right to rule and to use Ireland as a base to recover his throne. Back in Scotland, Dundee was declared an outlaw and Mackay, now major-general for the army in Scotland, set out to arrest him. Dundee learned of Mackay's approach and with a small party of followers, rode north. Many of the Highland clans were loyal to the House of Stuart and Dundee set about organizing them into a force to retake Scotland for James. All through the spring and early summer of 1689, Dundee visited or wrote to the clan chiefs urging them to join him in this effort. The letter shown below is a facsimile of one of several that he sent to Clunie. It resulted in about 200 Macphersons joining Dundee in June and skirmishing with a detachment of Mackay's forces farther down the Spey.
The first real battle of the rebellion came at the Pass of Killiecrankie on 27 July 1689. Blair Castle and the base at Inverlochy had been seized by loyal clansmen and Mackay marched north from Stirling to recapture them. The path through the gorge was only wide enough for three men abreast or a single pack horse so it took all day for the force of 4000 men and 1200 pack horses to complete the passage. When leading elements of Mackay's force emerged they found Dundee's Highlanders arrayed on the high ground to their right and the Garry river to their left. As the sun set, the Highlanders charged down the hill, and after discharging their muskets, attacked the Williamite force with broadswords, sweeping it away. The Pass was choked with pack horses and the survivors were massacred with only Mackay and about 400 others managing to escape.
Dundee had led the charge but fell dying from a musket ball that pierced his body armour as indicated in the drawing below. He was taken to the Blair Athole church where he died and was buried. His death was a grave loss for the Jacobites because there was no leader with comparable skill to lead the Clans who often mistrusted each other more than their enemies. Duncan of Cluny had played a waiting game and the Macphersons arrived at Blair two days later.
There were other battles but the only one in which the Macphersons were involved was at the Haughs of Cromdale on 1 May 1690 when 200 of them were part of a force under Major-General Thomas Buchan that was surprised. 25 were killed including William Bàn, brother of William of Invereshie. James' cause came to nothing when his forces in Ireland suffered a disastrous defeat at the Battle of the Boyne on 1 July 1690. In 1696, Duncan found himself imprisoned in Inverlochy Castle for his participation in the insurrection.