King William was anxious to win the support of the Scottish bishops (as he had done with the English bishops) and met the Bishop of Edinburgh, Alexander Rose, in London.
The king said “I hope you will be kind to me and follow the example of England”. The Jacobite bishop replied “Sir, I will serve you as far as law, reason or conscience shall allow me.” It was an answer which did not impress the king.
The bishops had a second chance, however, when the Convention met in Edinburgh in 1689. The Duke of Hamilton assured it that nothing would be done which would harm the Episcopal Church if the bishops would give the same support to the king as the English bishops were doing.
However, the bishops decided that they could not break the oaths they had given to King James and so Episcopacy was disestablished and the Church in Scotland became Presbyterian once more.
Change was slow and even by 1707 (the year in which the Scots Parliament began an adjournment that was to last until 1999) there were still 165 Episcopalian priests ministering in the parish churches of Scotland.
Queen Anne, who succeeded William and Mary in 1702, was a pious, Anglican woman, who had much sympathy for the Episcopal Church in Scotland. She wrote to the Scottish Privy Council saying that Episcopalians should be protected in the peaceful exercise of their religion.
The Act of Toleration in 1712 gave protection to Episcopalians who were prepared to forsake the House of Stuart. They were able to worship freely, using the English Liturgy, and during the 18th century the number of such Qualified Congregations grew. It was not until the 19th century that they began to be reunited with the Scottish bishops and the other congregations of the Church. (The last to do so was a church in Montrose, which became part of the Diocese of Brechin in 1920).
However, as the number of congregations qualified under the 1712 Act grew there was a decline in the fortunes of those non-jurors who could not in conscience accept, and the crisis came with the death of Queen Anne in 1714.