Parliament was soon hindered by dissension within this military leadership. These officers were not professional soldiers; their experience and skill at warfare varied. More significantly, a faction of them avoided engagements with the Cavalier forces, hoping that reconciliation with King Charles I was still possible. Lord Manchester, perhaps the most prominent of these, expressed his pessimism for the war as follows: If we beat the king 99 times he is still king, and so will his posterity be after him; but if the king beat us once, we shall all be hanged, and our posterity be made slaves.
As the war proceeded, it was clear that Essex and Manchester were at best half-hearted in pursuing the fight against the royalists, an attitude that became ever more apparent as the struggle became more radical. The growing rift between the Lords and the Commons finally came to a point of crisis when the fruits of the great victory at the battle of Marston Moor were allowed to slip away at the disappointing second battle of Newbury. It was after this that the political tensions between Cromwell and Manchester could no longer be contained by the established forms of command.
Members of Parliament, notably Oliver Cromwell and Sir William Waller, saw the need for radical reform of the army. For Cromwell, this attack on Manchester's conduct ultimately became an attack on the Lords, most of whom held the same views as Manchester, and on the Scots, who attempted to bring Cromwell to trial as an "incendiary". At the height of this bitter controversy, Cromwell suddenly proposed to stifle all animosities by the resignation of all officers who were members of either House. This proposal, in theory, affected himself no less than the Earls of Essex and Manchester.
A second version of the bill was prepared, which required resignations as above, but did not forbid re-appointment of the officers. This bill was agreed to on April 3, 1645. The text of the second Ordinance can be found here
In practical terms, the Ordinance solidified the power of Cromwell and his “war party” faction. Cromwell was a member of the House of Commons, so he was obligated to resign his post as well. However, the Committee of Both Kingdoms, which oversaw the war, found his talents as a soldier indispensable. His term in command was extended several times, in forty-day increments, until it was finally made permanent. While this appointment was officially as Fairfax’s lieutenant general, Cromwell wielded influence well beyond his rank.
More broadly, this reform helped usher in Cromwell’s New Model Army. This reorganized force, designed for unity and efficiency, incorporated several practices recognizable in modern armies. In addition to a professional officer corps promoted on merit, it replaced the sometimes balky local units with nationally controlled regiments, standardized training protocols, and ensured regular salary payments to the troops. This army soon turned the war in favor of Parliament, decisively beating the Royalist forces at the battle of Naseby on June 14, 1645.