Goodwin's sequestration was indicative of an escalating civil war among the godly. The initial panic over gathered churches was now being displaced by an even greater alarm over heresy. The Puritan clergy bewailed the rapid rise of Antinomianism, Arminianism, Anti-Scripturism, Socinianism, Familism and other pernicious errors. Heresiographers rushed into print with voluminous catalogues of contemporary sects and heresies. In Fast Sermons to Parliament, the Presbyterians implored the magistrate to crush heresies and schisms, and introduced a Blasphemy Ordinance in Parliament prescribing capital punishment for anti-Trinitarians and imprisonment for Arminians and other heretics. The City Presbyterians declared open season on sects and heresies, and identified Goodwin as Public Enemy No. 1. As the Leveller Humphrey Brooke commented, the Presbyterians styled Goodwin ‘The Grand Heretick of England’.

Stung by such bitter attacks, Goodwin responded in three major ways. Firstly, he sought to demonstrate his own soundness by combating heresy through preaching and writing. He lectured against Antinomians, Anabaptists and Seekers and devoted months of sermons to a critique of the Anti-Scripturists, which resulted in a major work of apologetics, The Divine Authority of the Scriptures Asserted. Secondly, in a series of tracts culminating in Hagiomastix, Goodwin challenged the Blasphemy Ordinance with sceptical arguments, and developed his tolerationist critique of the use of force in religion. Finally, Goodwin threw his weight behind the New Model Army. With the political Presbyterians dominant in both the City and Westminster, the army emerged as the one reliable protector of the radical Puritan minorities.