Most Confederates professed loyalty to Charles I of England in the belief they could reach a lasting settlement in return for helping defeat his opponents in the Wars of the Three Kingdoms.

The declared aims of the Confederates were similar to those of Sir Phelim O'Neill, the leader of the early stages of the rebellion in Ulster, who issued the Proclamation of Dungannon in October 1641.

On 22 March, at a synod in nearby Kells chaired by Hugh O'Reilly, Archbishop of Armagh, a majority of the Catholic bishops proclaimed that the rebellion was a just war.

The synod sent agents to France, Spain and Italy to gain support, gather funds and weapons, and recruit Irishmen serving in foreign armies.

[16] The Supreme Council also made its own seal, described as follows: "'Twas circular, and in its centre was a large cross, the base of which rested on a flaming heart, while its apex was overlapped by the wings of a dove.

[20] The last piece of legislation agreed by Charles I and Parliament was the 1642 Adventurers' Act, which provided funds to suppress the 1641 Rebellion by confiscating "rebel" lands.

In order to keep their estates, in the context of the Wars of the Three Kingdoms the Confederates claimed to be Royalists loyal to the king, which made reaching an agreement with him a matter of primary importance.

Confederate political demands included Irish self-government, secure tenure of their lands, amnesty for any acts committed during the Rebellion, an equal share in government positions and that these concessions be ratified by a post-war Parliament.

In terms of religion, they insisted on toleration of Catholicism and in June 1645 added the stipulation that the Catholic clergy should retain all properties taken from the Church of Ireland since 1641.

[22] The Confederate position was further weakened by divisions between the Old English, mostly descendants of those who arrived during the Anglo-Norman invasion of Ireland in 1172, and the native Gaelic Irish.

In general, the Old English wanted to regain the power and influence they had lost under the Tudors and although they were sincere Catholics, did not support establishing the church as the state religion.

[23] Gaelic Irish leaders such as Owen Roe O'Neill wanted to reverse the Plantations of Ireland, since this was the only way to retrieve their ancestral lands; however, they were far less united in their demands than the Old English and it has been argued they formed a pressure group, rather than a distinct political philosophy.

[23] In September 1643, the Confederates negotiated a "cessation" with James Butler, 1st Duke of Ormonde, Royalist Governor of Ireland, which was signed at Jigginstown, near Naas.

However, Murrough O'Brien, 1st Earl of Inchiquin, a rare Gaelic Irish Protestant who commanded the Royalist garrison of Cork, objected to the ceasefire and declared his allegiance to Parliament in England.

The Confederates received modest subsidies from the monarchies of France and Spain, who wanted to recruit troops in Ireland but their main continental support came from the Papacy.

Pope Innocent X strongly supported Confederate Ireland, over the objections of Cardinal Mazarin and the Queen, Henrietta Maria, who had moved to Paris in 1644.

Innocent received the Confederation's envoy in February 1645 and resolved to send a nuncio extraordinary to Ireland, Giovanni Battista Rinuccini, archbishop of Fermo, who embarked from La Rochelle with the Confederacy's secretary, Richard Bellings.

The Supreme Council put great hope in a secret treaty they had concluded with Edward Somerset, 2nd Marquess of Worcester, under his new title of Earl of Glamorgan, on the King's behalf, which promised further concessions to Irish Catholics in the future.

Under its terms Catholics would be allowed to serve in public office and to found schools; there were also verbal promises of future concessions on religious toleration.

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 the public practice of Catholicism was not guaranteed.

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 the papal nuncio Rinuccini 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.

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.

The Papal Nuncio, Rinuccini, endeavoured to uphold Owen Roe O'Neill by excommunicating all who in May 1648 took part in the Inchiquin Truce with the Royalists; but he could not get the Irish Catholic Bishops to agree on the matter.

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.

Given their large notional power base, the Confederates ultimately failed to manage and reorganise Ireland so as to defend the interests of Irish Catholics.