During the Civil Wars, the Puritan MPs of the Long Parliament were split broadly into two camps: the Independents and the Presbyterians. The division was primarily along religious lines, but was also reflected in differing political attitudes.
The Independents advocated freedom of religion for non-Catholics and the complete separation of church and state. With the collapse of Episcopalian church government during the 1640s, individual congregations gathered around their ministers (hence they are sometimes known as the "gathered" churches). The Independent congregations tended to limit their membership to true believers, sometimes to the extent of forming inner circles of godly parishioners who held separate meetings. The Independents' rejection of state-regulated worship brought them into conflict with the Presbyterians, who preferred a structured system of church government and were intolerant of non-conformists. Independent congregations were found mostly in south-eastern England. Although relatively few in number, the Independents wielded considerable influence in Parliament and among senior army officers.
During the First Civil War, an alliance between supporters of the "War Party" led by John Pym and moderate MPs brought the Independent faction to prominence in Parliament. The Independents favoured confrontation with the King and an outright military victory rather than the negotiated settlement sought by the Presbyterians of the "Peace Party". The Independents actively supported the military alliance with Scotland in 1644 and the re-organisation of the armed forces that resulted in the formation of the New Model Army in 1645.
Support for the Independents declined after the First Civil War when moderates became concerned that the radicals were threatening to make too many changes in church, state and society. The Second Civil War exacerbated the differences between the factions. Moderate support swung back to the Presbyterians who sought a treaty with the King and opposed Independent demands that he should be brought to justice for inflicting a second war upon the nation. Crucially, the New Model Army supported the Independent position and intervened to oust Presbyterian sympathisers from Parliament in Pride's Purge (December 1648).
After Pride's Purge, the so-called Rump Parliament of around 50 Independent MPs sanctioned the trial and execution of King Charles in January 1649 and the creation of the republican English Commonwealth.