In the middle of the century, matters became increasingly complicated as Charles I and the Parliament in England moved towards civil war.  The Old English and the remains of the native Irish leadership viewed loyalty to the crown as a means of gaining better conditions if the king were to triumph over Parliament.  Most Protestants in the Irish Parliament sided with the English Parliamentary forces as did most of the Ulster settlers.

In 1641 a rebellion broke out in both Dublin and Ulster.  The Old English in the South Joined with the native Irish in the North on the common ground of religion; thereafter they became indistinguishable in English eyes.  While some tension remained in the relationship between the two Irish groups, the distinction between them became increasingly unimportant.

The rebellion was confused and ultimately unsuccessful.  Initial successes near Drogheda were allied with atrocities perpetrated against the planter population in Ulster; one particularly horrific incident culminating 1n the drowning of hundreds of Protestant men, women and children in the Bann river near Portadown.

In 1642 leading Catholics convened a council at Kilkenny and set up a provisional government: the Confederation of Kilkenny.  The regular Parliament in Dublin expelled its remaining Catholic members.  The king, eager to retain the support of the Irish Parliament tried to neutralise the Irish Confederation by seeking a truce.  This was seen by many Protestants as evidence that the king had sympathy with Catholicism.  In the confusion the bishops, later joined by leading Catholic laymen, declared that the “insurgents”* war against the “puritans”** was a just one.

They excommunicated*** anyone who continued to support the puritans since they believed that the puritans aims were to destroy the Irish and the Catholic Faith.  They drafted an “oath of Association”, modelled on the Scottish Covenant.  This proclaimed allegiance to the Roman Church as well as a determination to uphold any special privileges the king had given them alongside the power of the Parliament of “this realm”.  They promoted the free exercise of the Catholic Faith and obedience to the “fundamental laws of Ireland”.  Finally they pledged to obey “the supreme council of the confederate Catholics of this kingdom”.

In 1643 a truce was signed with the king but this only served to alarm Protestants and further alienate them from the crown.  When the English civil war culminated in the execution of Charles, Oliver Cromwell came to Ireland in 1649 to restore Parliamentary rule.  He viewed his mission as a spiritual as well as a military crusade in which he claimed: “We, came, by the assistance of God, to hold forth and maintain the lustre and glory of English liberty in a nation where we have an undoubted right to do it”.  In both Drogheda and Wexford, Cromwell showed no quarter as the besieged**** inhabitants were slaughtered by his victorious troops in what he described as “a marvellous great mercy” avenging the “slaughtered saints” of 1641.  The ensuing settlement imposed on the Irish was harsh and included a prohibition on Catholic public worship and the outlawing of priests.  The events of the 1640s have left an enduring legacy in Ireland: the massacre of Protestants in1641, backed by Catholic bishops' statements and the atrocities perpetrated by Cromwell in the name of Protestantism are still very much alive in the hearts of many Protestants and Catholic within Ireland today.

* insurgent -  rising in revolt.  A person who rises in opposition to established authority; a rebel.

** Puritan - a person who in the time of Elizabeth and the Stuarts wished to carry the reformation of the Church of England further by purifying it of ceremony; an opponent of the Church of England on account of its retention of much of the ritual and belief of the Roman Catholics.

*** excommunicate -  to forbid or expel from the communion of (any branch of) the church; to deprive of church privileges.

**** besiege -  to lay siege to, to attack violently and surround with the intent of capturing; to attack and surround with armed forces.