The war being now over, the great question of the establishment of Presbyterianism or Independency had to be decided. Cromwell, without naming himself an adherent of any denomination, fought vigorously for Independency as a policy. In 1644 he had remonstrated at the removal by Crawford of an anabaptist lieutenant-colonel. "The state," he said, "in choosing men to serve it, takes no notice of their opinions. If they be willing faithfully to serve it, that satisfies. Take heed of being sharp ... against those to whom you can object little but that they square not with you in every opinion concerning matters of religion." He had patronized Lilburne and welcomed all into his regiment, and the Independents had spread from his troops throughout the whole army. But while the sectarians were in a vast majority in the army, the parliament was equally strong in Presbyterianism and opposed to toleration. The proposed disbandment of the army in February 1647 would have placed the soldiers entirely in the power of the parliament; while the negotiations of the king, first with the Scots and then with the parliament, appeared to hazard all the fruits of victory. The petition from the army to the parliament for arrears of pay was suppressed and the petitioners declared enemies of the state. In consequence the army organized a systematic opposition, and elected representatives styled Agitators or Agents to urge their claims.
Cromwell, though greatly disliking the policy of the Presbyterians, yet gave little support at first to the army in resisting parliament. In May 1647 in company with Skippon, Ireton and Fleetwood, he visited the army, inquired into and reported on the grievances, and endeavoured to persuade them to submit to the parliament. "If that authority falls to nothing," he said, "nothing can follow but confusion." The Presbyterians, however, now engaged in a plan for restoring the king under their own control, and by the means of a Scottish army, forced on their policy, and on the 27th of May ordered the immediate disbandment of the army, without any guarantee for the payment of arrears. A mutiny was the consequence. The soldiers refused to disband, and on the 3rd of June Cromwell, whom, it was believed, the parliament intended to arrest, joined the army. "If he would not forthwith come and lead them," they had told him, "they would go their own way without him." The supremacy of the army without a guiding hand meant anarchy, that of the Presbyterians the outbreak of another civil war.