Rinuccini became the dominant figure of the hard-line Clerical Faction of the Confederates refusing the alliance with the Irish Royalists.

Returning to serve his uncle at Rome, although a fever, perhaps malaria,[citation needed] permanently damaged his health, he won distinction as an advocate in the ecclesiastical courts, was named a camariere (chamberlain) by Pope Gregory XV and in 1625 became Archbishop of Fermo.

Rinuccini had sent ahead arms and ammunition: 1,000 braces of pistols, 4,000 cartridge belts, 2000 swords, 500 muskets and 20,000 pounds of gunpowder.

Rinuccini hoped that by doing so he could influence the Confederates' strategic policy away from making a deal with Charles I and the Royalists in the English Civil War and towards the foundation of an independent Catholic-ruled Ireland.

However, apart from some military successes such as the Battle of Benburb on 5 June 1646, the main result of Rinuccini's efforts was to aggravate the infighting between factions within the Confederates.

Alleging that he had been deliberately deceived, Rinuccini publicly backed the militant faction, which included most of the Catholic clergy and some Irish military commanders such as Owen Roe O'Neill; on the other side there were the Franciscans Pierre Marchant, and later Raymond Caron.

In 1646, when the Supreme Council tried to get the Ormond Peace ratified, Rinuccini excommunicated them and helped to get the Treaty voted down in the Confederate General Assembly.

However, the following year, the Confederates' attempts to drive the remaining English (mainly Parliamentarian) armies from Ireland met with disaster at the battles of Dungans Hill on 8 August 1647 and Knocknanuss on 13 November 1647.

[16] As a result, the chastened Confederates hastily concluded a new deal with the English Royalists to try to prevent a Parliamentarian conquest of Ireland in 1648.

Rinuccini backed Owen Roe O'Neill, who used his Ulster army to fight against his former comrades who had accepted the deal.

Rinuccini returned to Rome in November 1649 where he presented the Pope with a repport entitled "Relazione delle cose in Irlanda", which recounts his stay in Ireland in 36 chapters.