Confederate Ireland refers to the period of Irish self-government between the Rebellion of 1641 and the Cromwellian conquest of Ireland in 1649. During this time, two-thirds of Ireland was governed by the Irish Catholic Confederation, also known as the "Confederation of Kilkenny" (based in the city of Kilkenny). The remaining Protestant enclaves in Ulster, Munster and Leinster were held by armies loyal to the royalists, parliamentarians or Scottish Covenanters during the Wars of the Three Kingdoms. The Confederates failed to defeat the British armies in Ireland in 1642–49 in a conflict known as the Irish Confederate Wars and joined a royalist alliance in 1648 against the Rump Parliament.
The Confederate's stated objective was to reach an agreement with the King. The ambitions were: full rights for Catholics in Ireland, toleration of the Catholic religion, and self-government for Ireland. The motto of the Confederation was Pro Deo, Rege et Patria, Hibernia Unanimis (For God, King and Fatherland, Ireland is United).
The members of the Supreme Council were predominantly of Old English descent and were distrusted by many of the Gaelic Irish, who felt they were too moderate in their demands. The more radical Confederates pressed for a reversal of the plantations and the establishment of Catholicism as state religion in Ireland.
The Confederates believed that their aspirations were best served by alliance with the royalist cause and therefore made supporting the King a central part of their strategy. This was because the English Parliament and Scottish Covenanters had threatened before the war to invade Ireland and destroy the Catholic religion and Irish land-owning class. The King, by contrast, had repeatedly promised them some concessions. The difficulty for Charles was that he was horrified at the 1641 rebellion and had signed the Adventurers Act into law in 1642, which proposed confiscating all rebel held lands in Ireland. A new policy of refusing pardon to any Irish rebels had also been agreed in London and Dublin (issuing pardons had been a common method to end Irish conflicts in the previous century). Therefore his forces remained hostile to the Confederates until 1643, when his military position in England started to weaken. Many of the Confederate gentry stood to lose their land under the Adventurers Act; it galvanized their efforts and they realized that it could only be repealed by taking a loyal stance.
However, while the moderate Confederates were anxious to come to an agreement with Charles I and did not press for radical political and religious reforms, others wished to force the King to accept a self-governing Catholic Ireland before they came to terms with him. Failing that, they advocated an independent alliance with France or Spain.
In 1644, the Confederates sent around 1,500 men under Alasdair MacColla to Scotland to support the royalists there under James Graham, 1st Marquess of Montrose against the Covenanters, sparking a Civil War — their only intervention on the Royalist side in the civil wars in Britain.
The nuncio considered himself the virtual head of the Confederate Catholic party in Ireland. By March 1646, however, the Supreme Council of the Confederates had come to an agreement with Ormonde, signed March 28 1646. Under its terms Catholics would be allowed to serve in public office and found schools; there were also verbal promises of future concessions on religious toleration. There was an amnesty for acts committed in the Rebellion of 1641 and a guarantee against further seizure of Irish Catholic land. The Supreme Council also put great hope in a secret treaty they had concluded with the Earl of Glamorgan on the King's behalf, which promised further concessions to Irish Catholics in the future.
However, there was no reversal of Poynings Law which subordinated the Irish Parliament to the English one, no reversal of the Protestant domination of Parliament and no reversal of the main plantations, or colonisation, in Ulster and Munster. Moreover, regarding the religious articles of the treaty, all churches taken over by Catholics in the war would have to be returned to Protestant hands and public practice of Catholicism was not guaranteed.
In return for the concessions that were made Irish troops would be sent to England to fight for the royalists in the English Civil War. However, the terms agreed were not acceptable to either the Catholic clergy, the Irish military commanders — notably Owen Roe O'Neill and Thomas Preston — or the majority of the General Assembly. Nor was Rinuccini the papal nuncio party to the treaty, which left untouched the objects of his mission; he had induced nine of the Irish bishops to sign a protest against any arrangement with Ormonde or the king that would not guarantee the maintenance of the Catholic religion.
Many believed the Supreme Council were unreliable, since many of them were related to Ormonde or otherwise bound to him. Besides, it was pointed out that the English Civil War had already been decided in the English Parliament’s favour and that sending Irish troops to the royalists would be a futile sacrifice. On the other hand, many felt after O’Neill’s Ulster army defeated the Scots at the battle of Benburb in June 1646 that the Confederates were in a position to re-conquer all of Ireland. Furthermore, those who opposed the peace were backed, both spiritually and financially, by Rinuccini, who threatened to excommunicate the "peace party". The Supreme Council were arrested and the General Assembly voted to reject the deal.
These setbacks made most Confederates much more eager to come to reach an agreement with the royalists and negotiations were re-opened. The Supreme Council got generous terms from Charles I and Ormonde, including toleration of the Catholic religion, a commitment to repealing Poynings Law (and therefore to Irish self-government), recognition of lands taken by Irish Catholics during the war and a commitment to a partial reversal of the Plantation of Ulster. In addition, there was to be an Act of Oblivion, or amnesty for all acts committed during the 1641 rebellion and Confederate wars — in particular the killings of British Protestant settlers in 1641 — and the Confederate armies would remain in existence.
However Charles granted these terms only out of desperation and later repudiated them. Under the terms of the agreement, the Confederation was to dissolve itself, place its troops under royalist commanders and accept English royalist troops. Inchiquin also defected from the Parliament and rejoined the royalists in Ireland.
However, many of the Irish Catholics continued to reject a deal with the royalists. Owen Roe O'Neill refused to join the new royalist alliance and fought a brief internal civil war with the royalists and Confederates in the summer of 1648. So alienated was O'Neill by what he considered to be a betrayal of Catholic war aims that he tried to make a separate peace with the English Parliament and was for a short time effectively an ally of the English parliamentary armies in Ireland. This was disastrous for the wider aims of the Confederacy, as it coincided with the outbreak of the second civil war in England. The Papal Nuncio, Rinuccini, endeavored to uphold Owen Roe O'Neill by excommunicating all who took part in a truce with the Royalists; but he could not get the Irish Catholic Bishops to agree on the matter. On February 23, 1649, he embarked at Galway, in his own frigate, to return to Rome.
It is often argued that this split within the Confederate ranks represented a split between Gaelic Irish and Old English. It is suggested that a particular reason for this was that Gaelic Irish had lost much land and power since the English conquest of Ireland and hence had become radical in their demands. However, there were members of both ethnicities on either side. For example, Phelim O’Neill, the Gaelic Irish instigator of the Rebellion of 1641, sided with the moderates, whereas the predominantly Old English south Wexford area rejected the peace. The Catholic clergy were also split over the issue.
The real significance of the split was between those landed gentry who were prepared to compromise with the royalists as long as their lands and civil rights were guaranteed, and those, such as Owen Roe O'Neill, who wanted to completely overturn the British presence in Ireland. They wanted an independent, Catholic Ireland, with the British settlers expelled permanently. Many of the militants were most concerned with recovering ancestral lands their families had lost in the plantations. After inconclusive skirmishing with the Confederates, Owen Roe O'Neill retreated to Ulster and did not rejoin his former comrades until Cromwell’s invasion of 1649. This infighting fatally hampered the preparations of the Confederate-royalist alliance to repel the invasion of parliamentarian New Model Army.
Oliver Cromwell invaded Ireland in 1649 to crush the new alliance of Irish Confederates and royalists. The Cromwellian conquest of Ireland was the bloodiest warfare that had ever occurred in the country and was accompanied by plague and famine. It ended in total defeat for the Irish Catholics and royalists. Most of the senior members of the Confederation spent the Cromwellian period in exile in France, with the English Royalist Court. After the Restoration, those Confederates who had promoted alliance with the Royalists found themselves in favour and recovered their lands. However, those who remained in Ireland throughout the Interregnum invariably had all their land confiscated and in many cases were executed or transported to penal colonies. The pre-war Irish Catholic land-owning class was all but totally destroyed in this period, as were the institutions of the Roman Catholic Church.