The Confederates send around fifteen hundred men under Alasdair MacColla to Scotland in 1644 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 Confederates receive modest subsidies from the monarchies of France and Spain, who want to recruit troops in Ireland but their main continental support comes from the Papacy.

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

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

He had taken with him a large quantity of arms and military supplies and a very large sum of money.

These supplies mean that Rinuccini has a big influence on the Confederate's internal politics; he is backed by the more militant Confederates such as Owen Roe O'Neill.

Rinuccini is received at Kilkenny with great honors, asserting that the object of his mission is to sustain the King, but above all to help the Catholic people of Ireland in securing the free and public exercise of the Catholic religion, and the restoration of the churches and church property, but not any former monastic property.

The nuncio considers himself the virtual head of the Confederate Catholic party in Ireland.

The Supreme Council of the Confederates has come to an agreement with Ormonde, signed March 28, 1646.

Under its terms, Catholics will be allowed to serve in public office and find schools; there are also verbal promises of future concessions on religious toleration.

There is an amnesty for acts committed in the Rebellion of 1641 and a guarantee against further seizure of Irish Catholic land.

The Supreme Council also puts great hope in a secret treaty they have concluded with the Earl of Glamorgan on the King's behalf, which promises further concessions to Irish Catholics in the future.

However, there is no reversal of Poynings Law which subordinates the Irish Parliament to the English one, no reversal of the Protestant domination of Parliament and no reversal of the main plantations, or colonization, in Ulster and Munster.

Moreover, regarding the religious articles of the treaty, all churches taken over by Catholics in the war will have to be returned to Protestant hands and public practice of Catholicism is not guaranteed.

In return for the concessions that are made, Irish troops are to be sent to England to fight for the royalists in the English Civil War.

However, the terms agreed are 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 is Rinuccini the papal nuncio party to the treaty, which leaves 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 will not guarantee the maintenance of the Catholic religion.