By 1653, Goodwin's intellectual journey was largely complete. He had changed his mind on ecclesiology, politics and theology, but his new positions were now firmly set. His mission during the rest of the 1650s was to propagate his vision of a truly reformed Protestantism.

To begin with, Goodwin was optimistic. The republic's triumphs over its foes promised a new era of stability and freedom, when the godly could complete the reformation without fear of regal tyranny and clerical uniformity. But Goodwin (like so many other radical Puritans) was to be disappointed. The factionalism of the godly dogged the republic in the 1650s as it had troubled Parliamentarianism in the 1640s. Goodwin's own congregation was afflicted by a painful schism. Despite his vigorous efforts, the promotion of Arminianism proved an uphill struggle. Even Oliver Cromwell, who had promised so much, came to be viewed as a betrayer of the revolutionary cause.

The Rump and ‘State Religion’

One reason for Goodwin's disillusionment lay in the persistent appeal of ‘State Religion’. Although the advocates of Presbyterian uniformity had been defeated, liberty of conscience was still threatened by a conservative Calvinism that wanted the state to police the boundaries of orthodoxy. In February 1652, a group of influential Independent clergy (led by John Owen) drew up a petition to be presented to Parliament. Owen and his colleagues were profoundly disturbed by the publication of the Socinians' Racovian Catechism (1651), and were determined to push for a government crackdown on heresy.