This chapter examines the fluctuating fortunes of the later Stuart churches in Scotland and Ireland. The precarious character of the 'national church' in the Stuart kingdoms was quickly exposed after James VII and II's accession in February 1685. The chapter outlines the legislative framework that determined ecclesiastical policy, and illustrates the extent to which the period was alternately characterised by periods of intense sectarianism and brutal suppression of nonconformists, alongside rival impulses towards comprehension and toleration. The chapter focuses on the relationship between statesmen and prelates in pulpits than on dissenters and narratives of persecution and unjustified tyranny. It shows recurrent interactions between the established churches and nonconformists from 1660 onwards, whether antagonistic or conciliatory, served to sharpen each denomination's self-understanding, enabling rival traditions to articulate their religious differences with greater precision by 1714.