Though wounded and for a time missing, in the end Mackinnon got back crippled to Isle aux Noix.  But he had failed, and whispers soon began that he showed cowardice in the attack; an absurd charge, as Nairne said, for he had given proof of rather too much, than of too little, courage.  The accusation gave Nairne infinite trouble.  The subalterns in the Royal Highland Emigrants refused to do duty with Mackinnon, and General Haldimand, who succeeded Carleton in the summer of 1778, would not take the matter seriously enough to grant a Court Martial, that Mackinnon might clear himself.  For quite a year and a half the affair dragged on.  In the end, at a Court of Enquiry, Mackinnon was acquitted.  Haldimand told Nairne to rebuke the officers sternly for combining to subvert authority, for disrespect to their superiors, and for refusing, on the basis of futile reports and hearsays, to serve with Mackinnon.  “I much mistake his character,” wrote Nairne of Mackinnon, “if he can ... be prevented from calling one or two of those gentlemen to a severe account.”

A part of Nairne’s duty was to watch the French Canadians and check sedition.  In spite of the failure of Arnold’s expedition many of them were still favourable to the American cause.  They harboured deserters in the remoter parishes, gave protection and assistance to rebels, and threw as many difficulties as possible in the path of loyalists.  Nairne found two men issuing papers from a printing press to foment sedition and sent them down to Quebec to stand their trial for treason.

From Isle aux Noix Nairne was sent, in the summer of 1779, with fifty of his Royal Highland Emigrants, to command at Carleton Island, near Kingston where Lake Ontario flows into the St. Lawrence; some thirty-five years later his only surviving son held a military command at the same place.  Here there was much to do in strengthening the fortifications and in keeping up communications with Niagara and other points in the interior.  The situation was not without its embarrassments.  Prisoners were sent in from Niagara and he had no prison in which to keep them.  For want of fresh meat and vegetables there was much sickness.  But the Indians were his greatest trial.  Through him came their supplies and, to hold them at all, he had sometimes to serve out the rum for which such savages are always greedy.  On July 4th, Nairne made a speech to these Mississaga Indians and said pretty plainly what he thought of them.  Against the American scouts they had proved no defence; at night they fired off guns in the neighbouring woods and created false alarms, which prevented Nairne’s men from getting their proper sleep.  “My men work hard in the day,” he said, “and I will have them to sleep sound at night,” and he warned the Indians that he would fire upon them if their noise disturbed him further.  The savages, he wrote to Haldimand, are “almost unbearable, greedy and importunate.”  They behaved more like rebels than friends and their talk ended always in the demand for rum, “the cause of all bad behaviour in Indians.”