Sometimes referred to as the "mopping up" operations,[2] many rebels, forced to come of out of hiding by a scorched earth campaign by government troops,[3][4] surrendered themselves and their arms, while others remained at large until they were captured and punished.

On 14 May, George Munro, 1st of Culcairn's company reached Fort Augustus and by this time there were rumours that the Jacobite leader, known as the Young Pretender (Charles Edward Stuart) had got off a French ship and had been on the isles of Harris and Lewis.

On 19 May, Major-general John Campbell wrote from Fort William that the rebel Jacobite Coll MacDonell of Barisdale had gone to Loch Arkaig with 120 men and that the Glengarry folk were to join him, that there were new arms and Lochgarry, the Macphersons and Frasers were also expected.

Lord Loudoun with the seventeen independent companies marched five miles from Fort Augustus to Aberchalder to make room for Prince William, Duke of Cumberland who was expected with the army.

Macrae gave information on the rebels gathering at Achnacarry, but Lord Loudoun considered him a spy and sent him to the Duke of Cumberland who was then still at Inverness.

[7] On 22 May 1746, Lord Loudoun with 300 regular troops, 250 men of the Campbell of Argyll Militia and eight Independent Highland Companies of the MacDonalds, Mackenzies, Rosses, Grants and Mackays marched down the Great Glen.

[9] On 24 May, Lord Loudoun almost captured the rebel Jacobite Donald Cameron of Lochiel who was forced to disperse his men and flee to Rannoch.

[10] On 10 June, Aeneas MacDonnell, brother of Kinlochmoidart, who had already been captured, finally admitted to Major-general Campbell that the Young Pretender had sailed to South Uist.

On 11 June, Munro of Culcairn marched with his seven companies from Moy to Linachan and at Inverness Lord Loudoun made a return of more than 2,000 firelocks collected in five weeks.

[10] On 13 June, the rebel Jacobite Coll MacDonell of Barisdale submitted at Glenelg and two days later he met Lord Loudoun and Sir Alexander MacDonald having been offered terms in exchange for information about the Young Pretender.

On 21 June MacLeod of Talisker crossed over to Skye and marched to Loch Bracadale where Bernera's, Aird's and Kirkibost's companies were to embark for South Uist.

On 8 July, Talisker hurried over to Mugstot in Trotternish having heard news that the Young Pretender had landed there on 29 June disguised in women's clothes.

On 10 July, General Campbell reached Skye from Barra having received information that the Young Pretender had left Portree along with the Laird of Mackinnon.

[14] MacDonald of Barrisdale made arrangements to meet Captain John Sutherland of Forse, but he claimed that he had waited at the rendezvous point but no one had turned up.

In the early hours of 20 September, the Young Pretender sailed from Loch nan Uamh having only had the under strength companies of Lord Loudoun's Regiment to contend with.