His task was not without difficulty.  It was indeed well known that the Estates were generally inclined to support the government.  But it was also well known that there was one subject which would require the most dexterous and delicate management.  The cry of the blood shed more than three years before in Glencoe had at length made itself heard.  Towards the close of the year 1693, the reports, which had at first been contemptuously derided as factious calumnies, began to be generally thought deserving of serious attention.  Many people little disposed to place confidence in any thing that came forth from the secret presses of the Jacobites owned that, for the honour of the government, some inquiry ought to be instituted.  The amiable Mary had been much shocked by what she heard.  William had, at her request, empowered the Duke of Hamilton and several other Scotchmen of note to investigate the whole matter.  But the Duke died; his colleagues were slack in the performance of their duty; and the King, who knew little and cared little about Scotland, forgot to urge them.594

It now appeared that the government would have done wisely as well as rightly by anticipating the wishes of the country.  The horrible story repeated by the nonjurors pertinaciously, confidently, and with so many circumstances as almost enforced belief, had at length roused all Scotland.  The sensibility of a people eminently patriotic was galled by the taunts of southern pamphleteers, who asked whether there was on the north of the Tweed, no law, no justice, no humanity, no spirit to demand redress even for the foulest wrongs.  Each of the two extreme parties, which were diametrically opposed to each other in general politics, was impelled by a peculiar feeling to call for inquiry.  The Jacobites were delighted by the prospect of being able to make out a case which would bring discredit on the usurper, and which might be set off against the many offences imputed by the Whigs to Claverhouse and Mackenzie.  The zealous Presbyterians were not less delighted at the prospect of being able to ruin the Master of Stair.  They had never forgotten or forgiven the service which he had rendered to the House of Stuart in the time of the persecution.  They knew that, though he had cordially concurred in the political revolution which had freed them from the hated dynasty, he had seen with displeasure that ecclesiastical revolution which was, in their view, even more important.  They knew that church government was with him merely an affair of State, and that, looking at it as an affair of State, he preferred the episcopal to the synodical model.  They could not without uneasiness see so adroit and eloquent an enemy of pure religion constantly attending the royal steps and constantly breathing counsel in the royal ear.  They were therefore impatient for an investigation, which, if one half of what was rumoured were true, must produce revelations fatal to the power and fame of the minister whom they distrusted.  Nor could that minister rely on the cordial support of all who held office under the Crown.  His genius and influence had excited the jealousy of many less successful courtiers, and especially of his fellow secretary, Johnstone.