In 1560, the Scottish Parliament abolished papal jurisdiction and approved Calvin's Confession of Faith, but did not accept many of the principles laid out in Knox's First Book of Discipline, which argued, amongst other things, that all of the assets of the old church should pass to the new.John Knox himself had no clear views on the office of bishop, preferring to see them renamed as 'superintendents'; but in response to the new Concordat a Presbyterian party emerged headed by Andrew Melville, the author of the Second Book of Discipline.This met vigorous opposition and he was forced to concede that the General Assembly should continue to run the church, but Presbyterians reacting against the formal liturgy were opposed by an Episcopalian faction.However, the Comprehension Act 1690 allowed episcopalian incumbents, on taking the Oath of Allegiance, to retain their benefices, though excluding them from any share in the government of the Church of Scotland without a further declaration of presbyterian principles.The excluded bishops were slow to organize the episcopalian remnant under a jurisdiction independent of the state, regarding the then arrangements as provisional, and looking forward to a reconstituted national episcopal Church under a 'legitimate' sovereign (see Jacobitism).The official recognition of George III on the death of Charles Edward Stuart in 1788, removed the chief bar to progress but the Episcopal Church had been reduced to no more than four bishops and about forty priests.The Scottish Communion Office, compiled by the non-jurors in accordance with primitive models, has had a varying co-ordinate authority, and the modifications of the English liturgy adopted by the American Church were mainly determined by its influence.No existing ministry can claim regular historic continuity with the ancient hierarchy of Scotland, but the bishops of the Episcopal Church are direct successors of the prelates consecrated to Scottish sees at the Restoration.
The death of Charles Edward Stuart led to better conditions for the growth of the church.