The Church of Scotland inherited the established status of the medieval church, but was fundamentally reformed into a Presbyterian polity in the late sixteenth century and again after 1688. It was more plausible to contend that the Reformation in Scotland had broken the link between church and crown, whereas in England that conclusion was harder to draw. Yet this key issue was not clear, since Episcopalians and Presbyterians remained locked in conflict for possession of a single Scots church. The episcopal system restored in 1660 was more of an attempt at compromise than its English parallel; it did not, for example, challenge existing presbyterial ordinations. Nonetheless, this solution failed, first in the face of armed resistance by the Presbyterian Covenanters, and again when the Scots bishops made clear the limits of their allegiance to William III. In 1690, the Presbyterian system was instituted by an act of the Scots parliament in an embittered setting,41 and the Presbyterian settlement was continually threatened by a possible Stuart Restoration for which the Episcopalians longed.

The Scots church had been subject to a much larger dose of Calvinism in the later sixteenth century than the English. Consequently it found it difficult to present itself as the church of all the Scots; its Genevanzeal cast it increasingly as a gathered church of the elect. It subscribed to what looked like a foundation document, the Westminster Confession of Faith, ratified by the Edinburgh parliament in 1647. The Confession was based on the Scottish Solemn League

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