While William’s first Parliament was debating, his enemies were entering upon a struggle which was destined to be brief. Edinburgh Castle held out for King James till June 14th, 1689, when its captain, the Duke of Gordon, capitulated. Graham of Claverhouse, now Viscount Dundee, had collected an army of Highlanders, against whom William sent General Mackay, a Scotsman who had served in Holland. Mackay followed Dundee through the Highlands to Elgin and on to Inverness, and finally, after many wanderings, the two armies met in the pass of Killiecrankie. Dundee and his Highlanders were victorious, but Dundee himself was killed in the battle, and his death proved a fatal blow to the Jacobite cause. After some delay Mackay was able to attain the object for which the battle had been fought—the possession of Blair Athole Castle. The military resistance soon came to an end.
The ecclesiastical settlement followed the suppression of the rebellion. The deprivation of nonjuring clergymen had been proceeding since the establishment of the new Government, and in 1690 an act was passed restoring to their parishes the Presbyterian clergy who had been ejected under Charles II. A small temporary provision was made for their successors, who were now, in turn, expelled. On the 26th May, 1690, the Parliament adopted the Confession of Faith, although it refused to be committed to the Covenant. The Presbyterian form of Church government was established; but King William succeeded in maintaining some check on the General Assembly, and toleration was granted to such Episcopalian dissenters as were willing to take the oath of allegiance. On the other hand, acceptance of the Confession of Faith was made a test for professors in the universities. The changes were carried out with little disturbance to the peace, there was no blood spilt, and except for some rough usage of Episcopalians in the west (known as the “rabbling of the curates"), there was nothing in the way of outrage or insult. The credit of the settlement belongs to William Carstares, afterwards Principal of the University of Edinburgh, whose tact and wisdom overcame many difficulties.