From the confederate perspective, the war from 1641 until the Cromwellian invasion in 1649 can be divided into a number of distinct phases. The first stage consisted of a confused populist uprising, which rapidly spread throughout the country. After some initial success, the rebels soon found themselves on the defensive as a result of a savage counter-offensive by the colonial administration in Dublin. Large numbers of troops were drafted from England, while in Ulster Monroe's Scottish army gained the upper hand. Confederate fortunes improved with the outbreak of the English civil war in August 1642, which diverted military supplies away from Ireland. The colonial government's offensive ground to a halt, enabling the confederates to organise their armies, assisted by veterans such as Owen Roe O'Neill and Thomas Preston who returned from the continent with men and equipment. In early 1643 confederate and royalist representatives initiated talks, which resulted in a cessation agreement in September. Thereafter, the bulk of royalist troops were shipped to England, and those who remained did not engage in further fighting.
September 1643 also witnessed the signing of the Solemn League and Covenant between the Scottish covenanters and the English parliamentarians. The covenanters committed themselves to intervening in the English civil war against the king. They also rejected the cessation agreement in Ireland. Between 1644 and 1646, the confederates mobilised their forces in a number of abortive campaigns against the Scots in Ulster and parliamentarians in Cork, while at the same time attempting to negotiate a permanent peace with the king's representative in Ireland, James Butler, marquis of Ormond.
A papal nuncio
In late 1645, with the confederate/royalist peace talks stalled on the issue of religious concessions to catholics, a papal nuncio, Giovanni Battista Rinuccini, arrived in Ireland advocating a full restoration of the Catholic Church. He also brought much needed cash to re-energise the war effort. In June 1646, Owen Roe O'Neill and his Ulster army won the greatest confederate victory of the war at Benburb, in eastern Tyrone, against Monroe and the covenanters. At this very moment, the confederates were plunged into crisis over the proposed peace terms with Charles I.
The king had surrendered to the Scots earlier in 1646, bringing to an end the first English civil war. Nonetheless, the confederate leadership in Kilkenny, anxious to rid itself of the stigma of rebellion, finally agreed to a treaty with Ormond which simply ignored the contentious issue of religion. The dominant peace faction hoped that a grateful monarch would grant generous concessions after he had recovered his authority in England. Rinuccini and the catholic bishops condemned the treaty and excommunicated those who supported it. The clerical faction staged a coup d'état in September 1646, seizing control in Kilkenny and imprisoning the leaders of the peace faction. The nuncio decided to attack the royalist headquarters at Dublin in an effort to bring the war in Ireland to a rapid conclusion. This would have enabled the confederates to negotiate from a position of strength with whoever controlled England. Rinuccini appointed Owen Roe O'Neill and his great rival Thomas Preston as dual commanders of this winter offensive. However, a combination of harsh weather, lack of supplies and bitter animosities between O'Neill and Preston served to undermine the campaign.