The news of the fight of Naseby reaching Coventry, Baxter, who had friends in the Parliamentary forces, wishing, as he says, to be assured of their safety, passed over to the stricken field, and spent a night with them. He was afflicted and confounded by the information which they gave him, that the victorious army was full of hot-headed schemers and levellers, who were against King and Church, prelacy and ritual, and who were for a free Commonwealth and freedom of religious belief and worship. He was appalled to find that the heresies of the Antinomians, Arminians, and Anabaptists had made sadder breaches in the ranks of Cromwell than the pikes of Jacob Astley, or the daggers of the roysterers who followed the mad charge of Rupert. Hastening back to Coventry, he called together his clerical brethren, and told them "the sad news of the corruption of the army." After much painful consideration of the matter, it was deemed best for Baxter to enter Cromwell's army, nominally as its chaplain, but really as the special representative of orthodoxy in politics and religion, against the democratic weavers and prophesying tailors who troubled it. He joined Whalley's regiment, and followed it through many a hot skirmish and siege. Personal fear was by no means one of Baxter's characteristics, and he bore himself through all with the coolness of an old campaigner. Intent upon his single object, he sat unmoved under the hail of cannon-shot from the walls of Bristol, confronted the well-plied culverins of Sherburne, charged side by side with Harrison upon Goring's musketeers at Langford, and heard the exulting thanksgiving of that grim enthusiast, when "with a loud voice he broke forth in praises of God, as one in rapture;" and marched, Bible in hand, with Cromwell himself, to the storming of Basing-House, so desperately defended by the Marquis of Winchester. In truth, these storms of outward conflict were to him of small moment. He was engaged in a sterner battle with spiritual principalities and powers, struggling with Satan himself in the guise of political levellers and Antinomian sowers of heresy. No antagonist was too high and none too low for him. Distrusting Cromwell, he sought to engage him in a discussion of certain points of abstract theology, wherein his soundness seemed questionable; but the wary chief baffled off the young disputant by tedious, unanswerable discourses about free grace, which Baxter admits were not unsavory to others, although the speaker himself had little understanding of the matter. At other times, he repelled his sad-visaged chaplain with unwelcome jests and rough, soldierly merriment; for he had "a vivacity, hilarity, and alacrity as another man hath when he hath taken a cup too much." Baxter says of him, complainingly, "he would not dispute with me at all." But, in the midst of such an army, he could not lack abundant opportunity for the exercise of his peculiar powers of argumentation. At Amersham, he had a sort of pitched battle with the contumacious soldiers. "When the public talking day came," says he, "I took the reading-pew, and Pitchford's cornet and troopers took the gallery. There did the leader of the Chesham men begin, and afterwards Pitchford's soldiers set in; and I alone disputed with them from morning until almost night; for I knew their trick, that if I had gone out first, they would have prated what boasting words they listed, and made the people believe that they had baffled me, or got the best; therefore I stayed it out till they first rose and went away." As usual in such cases, both parties claimed the victory. Baxter got thanks only from the King's adherents; "Pitchford's troops and the leader of the Chesham men" retired from their hard day's work, to enjoy the countenance and favor of Cromwell, as men after his own heart, faithful to the Houses and the Word, against kingcraft and prelacy.

Laughed at and held at arm's length by Cromwell, shunned by Harrison and Berry and other chief officers, opposed on all points by shrewd, earnest men, as ready for polemic controversy as for battle with the King's malignants, and who set off against his theological and metaphysical distinctions their own personal experiences and spiritual exercises, he had little to encourage him in his arduous labors. Alone in such a multitude, flushed with victory and glowing with religious enthusiasm, he earnestly begged his brother ministers to come to his aid. "If the army," said he, "had only ministers enough, who could have done such little as I did, all their plot might have been broken, and King, Parliament, and Religion might have been preserved." But no one volunteered to assist him, and the "plot" of revolution went on.

After Worcester fight he returned to Coventry, to make his report to the ministers assembled there. He told them of his labors and trials, of the growth of heresy and levelling principles in the army, and of the evident design of its leaders to pull down Church, King, and Ministers. He assured them that the day was at hand when all who were true to the King, Parliament, and Religion should come forth to oppose these leaders, and draw away their soldiers from them. For himself, he was willing to go back to the army, and labor there until the crisis of which he spoke had arrived. "Whereupon," says he, "they all voted me to go yet longer."

Fortunately for the cause of civil and religious freedom, the great body of the ministers, who disapproved of the ultraism of the victorious army, and sympathized with the defeated King, lacked the courage and devotedness of Baxter. Had they promptly seconded his efforts, although the restoration of the King might have been impossible at that late period, the horrors of civil war must have been greatly protracted. As it was, they preferred to remain at home, and let Baxter have the benefit of their prayers and good wishes. He returned to the army with the settled purpose, of causing its defection from Cromwell; but, by one of those dispensations which the latter used to call "births of Providence," he was stricken down with severe sickness. Baxter's own comments upon this passage in his life are not without interest. He says, God prevented his purposes in his last and chiefest opposition to the army; that he intended to take off or seduce from their officers the regiment with which he was connected, and then to have tried his persuasion upon the others. He says he afterwards found that his sickness was a mercy to himself, "for they were so strong and active, and I had been likely to have had small success in the attempt, and to have lost my life among them in their fury." He was right in this last conjecture; Oliver Cromwell would have had no scruples in making an example of a plotting priest; and "Pitchford's soldiers" might have been called upon to silence, with their muskets, the tough disputant who was proof against their tongues.

After a long and dubious illness, Baxter was so far restored as to be able to go back to his old parish at Kidderminster. Here, under the Protectorate of Cromwell, he remained in the full enjoyment of that religious liberty which he still stoutly condemned in its application to others.

He afterwards candidly admits, that, under the "Usurper," as he styles Cromwell, "he had such liberty and advantage to preach the Gospel with success, as he could not have under a King, to whom he had sworn and performed true subjection and obedience." Yet this did not prevent him from preaching and printing, "seasonably and moderately," against the Protector. "I declared," said he, "Cromwell and his adherents to be guilty of treason and rebellion, aggravated by perfidiousness and hypocrisy. But yet I did not think it my duty to rave against him in the pulpit, or to do this so unseasonably and imprudently as might irritate him to mischief. And the rather, because, as he kept up his approbation of a godly life in general, and of all that was good, except that which the interest of his sinful cause engaged him to be against. So I perceived that it was his design to do good in the main, and to promote the Gospel and the interests of godliness more than any had done before him."

Cromwell, if he heard of his diatribes against him, appears to have cared little for them. Lords Warwick and Broghill, on one occasion, brought him to preach before the Lord Protector. He seized the occasion to preach against the sentries, to condemn all who countenanced them, and to advocate the unity of the Church. Soon after, he was sent for by Cromwell, who made "a long and tedious speech" in the presence of three of his chief men, (one of whom, General Lambert, fell asleep the while,) asserting that God had owned his government in a signal manner. Baxter boldly replied to him, that he and his friends regarded the ancient monarchy as a blessing, and not an evil, and begged to know how that blessing was forfeited to England, and to whom that forfeiture was made. Cromwell, with some heat, made answer that it was no forfeiture, but that God had made the change. They afterwards held a long conference with respect to freedom of conscience, Cromwell defending his liberal policy, and Baxter opposing it. No one can read Baxter's own account of these interviews, without being deeply impressed with the generous and magnanimous spirit of the Lord Protector in tolerating the utmost freedom of speech on the part of one who openly denounced him as a traitor and usurper. Real greatness of mind could alone have risen above personal resentment under such circumstances of peculiar aggravation.

In the death of the Protector, the treachery of Monk, and the restoration of the King, Baxter and his Presbyterian friends believed that they saw the hand of a merciful Providence preparing the way for the best good of England and the Church. Always royalists, they had acted with the party opposed to the King from necessity rather than choice. Considering all that followed, one can scarcely avoid smiling over the extravagant jubilations of the Presbyterian divines, on the return of the royal debauchee to Whitehall. They hurried up to London with congratulations of formidable length and papers of solemn advice and counsel, to all which the careless monarch listened, with what patience he was master of. Baxter was one of the first to present himself at Court, and it is creditable to his heart rather than his judgment and discrimination that he seized the occasion to offer a long address to the King, expressive of his expectation that his Majesty would discountenance all sin and promote godliness, support the true exercise of Church discipline and cherish and hold up the hands of the faithful ministers of the Church. To all which Charles II. "made as gracious an answer as we could expect," says Baxter, "insomuch that old Mr. Ash burst out into tears of joy." Who doubts that the profligate King avenged himself as soon as the backs of his unwelcome visitors were fairly turned, by coarse jests and ribaldry, directed against a class of men whom he despised and hated, but towards whom reasons of policy dictated a show of civility and kindness?

There is reason to believe that Charles II., had he been able to effect his purpose, would have gone beyond Cromwell himself in the matter of religious toleration; in other words, he would have taken, in the outset of his reign, the very steps which cost his successor his crown, and procured the toleration of Catholics by a declaration of universal freedom in religion. But he was not in a situation to brave the opposition alike of Prelacy and Presbyterianism, and foiled in a scheme to which he was prompted by that vague, superstitious predilection for the Roman Catholic religion which at times struggled with his habitual scepticism, his next object was to rid himself of the importunities of sentries and the trouble of religious controversies by reestablishing the liturgy, and bribing or enforcing conformity to it on the part of the Presbyterians. The history of the successful execution of this purpose is familiar to all the readers of the plausible pages of Clarendon on the one side, or the complaining treatises of Neal and Calamy on the other.

Charles and his advisers triumphed, not so much through their own art, dissimulation, and bad faith as through the blind bigotry, divided counsels, and self-seeking of the Nonconformists. Seduction on one hand and threats on the other, the bribe of bishoprics, hatred of Independents and Quakers, and the terror of penal laws, broke the strength of Presbyterianism.