In English church history, Independents advocated local congregational control of religious and church matters, without any wider geographical hierarchy, either ecclesiastical or political. Independents reached particular prominence between 1642 and 1660, in the period of the English Civil War and of the Commonwealth and Protectorate, wherein the Parliamentary Army became the champion of Independent religious views against the Anglicanism or the Catholicism of Royalists and the Presbyterianism favoured by Parliament itself. The Independents advocated freedom of religion for non-Catholics and the complete separation of church and state.
During the First Civil War, the Parliamentary cause was supported by an alliance of Anglicans who supported Parliamentary traditions, Presbyterians and Independents. During the period leading up to war and during the early years of the First Civil War the Presbyterian party under the leadership of John Pym was in the ascendant. However as was shown the outcome of negotiations for an alliance with the Presbyterian Scots over the Solemn League and Covenant in 1643 the Independents party were strong enough to prevent Presbyterianism being imposed on them.
After the formation of the New Model Army the strength of the Independents grew along with the fortunes of the Army because Independents held many of the senior positions within the Army (Oliver Cromwell being the most famous of them). In 1648, at end of the Second Civil War the Independents in the Army were strong enough to remove from Parliament all those who opposed them in what has become known as Pride's Purge.
After Pride's Purge, the so-called Rump Parliament of around fifty Independent MPs sanctioned the trial and execution of King Charles in January 1649 and the creation of the republican English Commonwealth.
For the next decade the independents dominated English politics until shortly before the Restoration.
After the Restoration the Anglicans from both those who had supported the Parliamentary and Royalist causes dominated the English Parliament and imposed the Clarendon Code which combined with the Test Act, excluded all nonconformists from holding civil or military office, and prevented them from being awarded degrees by the universities of Cambridge and Oxford.