Act for securing the Protestant Religion and Presbyterian Church
Finally, the Treaty of Union refers to an Act of the Scots Parliament intitled ‘Act for securing the Protestant Religion and Presbyterian Church Government’.
This Act came at the end of the often bloody struggle for direction of the Church of Scotland. Since the Reformation led by John Knox, the Kirk had been firmly Protestant, but it retained its ancient structure of bishops and archbishops. Through the bishops though, and by the influence of the Church of England, forms of liturgy and ceremonies had been introduced, repellant to those who would ensure that the Church remained pure and with no words to govern worship but the Bible itself. At the Glorious Revolution of 1688, the presbyterian party, who opposed bishops, finally prevailed over the episcopalian party, which supported them: all forms of prelacy were abolished in Scotland by law and the Westminster Confession, which had been devised in Cromwell’s time to define the presbyterian settlement of the church, was made the fixed doctrine of the Church of Scotland.
The Episcopalians though were not giving up and the Presbyterians realised that a union with England, whose church was episcopal, could result in their settlement being overthrown. Therefore the commissioners sent to negotiate the Treaty were enjoined by law that they "should not treat of or concerning any Alteration of the Worship, Discipline, and Government of the Church of this Kingdom as now by Law established".
Therefore it was made a condition of the Union that the presbyterian organisation of the Church of Scotland be maintained, and further that "the Universities and Colledges of Saint Andrews, Glasgow, Aberdeen, and Edinburgh, as now established by Law, shall continue within this Kingdom forever" and that no one might be admitted as a professor or master unless they subscribed to the Confession of Faith, and further that each succeeding sovereign must subscribe to protect the presbyterian settlement of the Kirk.