The Tudor theory of its relation to the State, of its right to embrace all Englishmen within its pale, and to dictate what should be their faith and form of worship, remained utterly unquestioned by any man of note. The sentiments on which such a theory rested indeed for its main support, the power of historical tradition, the association of "dissidence " with danger to the State, the strong English instinct of order, the as strong English dislike of " innovations," with the abhorrence of "indifferency," as a sign of lukewarmness in matters of religion, had only been intensified by the earlier incidents of the struggle with the King. The Parliament therefore had steadily pressed on the new system of ecclesiastical government in the midst of the troubles of the war. An Assembly of Divines which was called together at Westminster in 1643, and which sat in the Jerusalem Chamber during the five years which followed, was directed to revise the Articles, to draw up a Confession of Faith, and a Directory of Public Worship; and these with a scheme of Church government, a scheme only distinguished from that of Scotland by the significant addition of a lay court of superior appeal set by Parliament over the whole system of Church courts and assemblies, were accepted by the Houses and embodied in a series of Ordinances.

Had the change been made at the moment when "with uplifted hands" the Commons swore to the Covenant in St. Margaret's it would probably have been accepted by the country at large. But it met with a very different welcome when it came at the end of the war. In spite of repeated votes of Parliament for its establishment, the pure Presbyterian system took root only in London and Lancashire. While the Divines, indeed, were drawing up their platform of uniform belief and worship in the Jerusalem Chamber, dissidence had grown into a religious power. In the terrible agony of the struggle against Charles, individual conviction became a stronger force than religious tradition. Theological speculation took an unprecedented boldness from the temper of the times. Four years after the war had begun a horror-stricken pamphleteer numbered sixteen religious sects as existing in defiance of the law; and, widely as these bodies differed among themselves, all were at one in repudiating any right of control in faith or worship by the Church or its clergy.

Milton himself had left his Presbyterian stand-point, and saw that "new Presbyter is but old Priest writ large." The question of sectarianism soon grew into a practical one from its bearing on the war: for the class specially infected with the new spirit of religious freedom was just the class to whose zeal and vigour the Parliament was forced to look for success in its struggle. We have seen the prevalence of this spirit among the farmers from whom Cromwell drew his horsemen, and his enlistment of these "sectaries " was the first direct breach in the old system of conformity. The sentiments of the farmers indeed were not his own. Cromwell had signed the Covenant, and there is no reason for crediting him with any aversion to Presbyterianism as a system of doctrine or of Church organization. His first step was a purely practical one, a step dictated by military necessities, and excused in his mind by a sympathy with "honest" men, as well as by the growing but still vague notion of a communion among Christians wider than that of outer conformity in worship or belief. But the alarm and remonstrances of the Presbyterians forced his mind rapidly forward on the path of toleration. "The State in choosing men to serve it," Cromwell wrote before Marston Moor, "takes no notice of these opinions.

If they be willing faithfully to serve it, that satisfies."Marston Moor spurred him to press on the Parliament the need of at least "tolerating " dissidents; and he succeeded in procuring the appointment of a Committee of the Commons to find some means of effecting this. But the conservative temper of the bulk of the Puritans was at last roused by his efforts. "We detest and abhor," wrote the London clergy in 1645, " the much endeavoured Toleration;" and the Corporation of London petitioned Parliament to suppress all sects " without toleration." The Parliament itself too remained steady on the conservative side. But the fortunes of the war told for religious freedom. Essex and his Presbyterians only marched from defeat to defeat. In remodelling the army the Commons had rejected a demand made by the Lords that officers and men, besides taking the Covenant, should submit " to the form of Church government that was already voted by both Houses." The victory of Naseby raised a wider question than that of mere toleration. "Honest men served you faithfully in this action," Cromwell wrote to the Speaker of the House of Commons from the field. "Sir, they are trusty: I beseech you in the name of God not to discourage them.

He that ventures his life for the liberty of his country, I wish he trust God for the liberty of his conscience." The storm of Bristol encouraged him to proclaim the new principles yet more distinctly. "Presbyterians, Independents, all here have the same spirit of faith and prayer, the same presence and answer. They agree here, have no names of difference; pity it is it should be otherwise anywhere. All that believe have the real unity, which is the most glorious, being the inward and spiritual, in the body and in the head. For being united in forms (commonly called uniformity), every Christian will for peace' sake study and do as far as conscience will permit And from brethren in things of the mind we look for no compulsion but that of light and reason".

The increasing firmness of Cromwell's language was due to the growing irritation of his opponents. The two parties became every day more clearly defined. The Presbyterian ministers complained bitterly of the increase of the sectaries, and denounced the toleration which had come into practical existence without sanction from the law. Scotland, whose army was still before Newark, pressed for the execution of the Covenant and the universal enforcement of a religious uniformity. Sir Harry Vane, on the other hand, was striving to bring the Parliament round to less rigid courses by the introduction of two hundred and thirty new members, who filled the seats left vacant by royalist secessions, and the more eminent of whom, such as Ireton and Algernon Sidney, were inclined to support the Independents. But it was only the pressure of the New Model, and the remonstrances of Cromwell as its mouthpiece, which hindered any effective movement towards persecution. Amidst the wreck of his fortunes Charles intrigued busily with both parties, and promised liberty of worship to Vane and the Independents, at the moment when he was negotiating with the Parliament and the Scots. His negotiations were quickened by the march of Fairfax upon Oxford. Driven from his last refuge, the King after some aimless wanderings made his appearance in the camp of the Scots. Lord Leven at once fell back with his royal prize to Newcastle. The new aspect of affairs threatened the party of religious freedom with ruin.