To co-ordinate their attack on their oppressors, the leading Irish chieftains had been called together by the Catholic clergy to create a grand Irish Catholic force called the Confederation of Kilkenny. The Roman Catholic clergy, many receiving orders from Rome, were the brains behind the operation.
The Confederation demanded full toleration for Roman Catholics and political self-government - ideas which were anathema to the King, Westminster Parliament and the Scottish Covenanters. Yet amazingly, this is what Ireland enjoyed during the 1640s - something which wouldn't be seen again until 1921.
The Confederation received an important morale boost from the return of the legendary Irish warlord, Owen Roe O'Neill. An inspirational soldier, glamorous chieftain and ardent Roman Catholic, he had spent the previous twenty years fighting the Catholic cause on the European mainland. Trained by the Spanish army, he would prove to be a brilliant commander for the Confederation and a loyal servant of the Vatican.
Opposing O'Neill was the Royalist commander in Dublin, James Butler, Earl of Ormond. An honourable but uncharismatic soldier and Old English aristocrat, he had the misfortune of fighting the Confederates with few resources and an appallingly ill-trained army. While the Gaelic Irish were inspired by religion and revenge, the Royalist force stood petrified. And Ormond was not the best man to inspire them.
Greater resistance came from a force of Scottish Presbyterians which had been sent over to Ulster. The Covenanters had been as terrified as the English by the Irish Rebellion and immediately offered a 10,000 strong army to quell the uprising. According to the Covenanters, 'unless we do fully vindicate these malicious papists [in Ireland], these two kingdoms both Scotland and England, cannot sleep long in security.' With the entry of the Presbyterian Scots into Ulster, the sectarian conflict in Ireland took a particularly brutal turn.
What made the conflict both frustrating and vicious was the nature of the warfare. The Confederates operated a brutal Viet-Cong style guerilla operation which entailed raiding parties and attacks on isolated outposts. At the few pitched battles there were, Ormond and the Scots forces did better. For the most part, the remaining settler communities were subjected to a brutal campaign of burning, looting and sporadic violence which tied down Ormond and the Scots. English, Scottish and Irish forces were now engaged in a bloody, fruitless skirmish on Irish soil which would last for years.