The rebellion had broken out in autumn 1641, with the rebel leaders issuing the
Proclamation of Dungannon declaring their aim of enhancing Catholic rights while declaring their continued loyalty to King
Charles I. Despite a failed attempt to seize Dublin Castle, the rebels enjoyed success across Ulster, and the uprising spread to other parts of the country. However, the rebels then suffered several defeats to the
Royal Irish Army and the Scottish
Covenanter Army in Ireland and by the time Eoghan Rua arrived, the rising was increasingly in trouble. , stated as being used by O'Neill in 1642 The subsequent war, known as the
Irish Confederate Wars, was part of the
Wars of the Three Kingdoms—civil wars throughout Britain and Ireland. Because of his military experience, O'Neill was recognised on his return to Ireland, at
Doe Castle in
County Donegal on 8 July 1642, as the leading representative of the O'Neills and head of the Ulster Irish. Sir Phelim O'Neill resigned the northern command of the Irish rebellion in Eoghan Rua's favour and escorted him from Lough Swilly to Charlemont. Upon arrival in Ireland, he received a letter from an English parliamentarian general by the name of Leslie, telling O'Neill that he was sad O'Neill, as an experienced officer, was committing himself to such a cause and that he should return to Spain. O'Neill responded that his cause in Ireland was far more honourable than an English general fighting against his own King. But distrust between the kinsmen was complicated by differences between Owen Roe O'Neill and the
Catholic Confederation which met at
Kilkenny in October 1642. Phelim professed to be acting in the interest of
Charles I; O'Neill's aim was complete independence of Ireland as a
Catholic country, while the
Old English Catholics represented by the council desired to secure religious liberty and an Irish constitution under English rule. O'Neill wanted the
Plantation of Ulster overturned and the recovery of the O'Neill dynasty's lands. The majority of Confederate military resources were directed to
Thomas Preston's Leinster Army. Preston, an Old English Catholic, was also a Spanish veteran but he and O'Neill had an intense personal dislike of each other. Mainly because Preston had been given the available military resources, O'Neill was outnumbered by the Scottish
Covenanter army that had landed in Ulster in 1642. He did, however, have a large number of experienced officers who had travelled with him from Flanders. The Irish Ulster Army, including regiments under
Rory Maguire, was poorly trained and undisciplined, so O'Neill set out to transform the army into a respectable force. Following a defeat at the
Battle of Clones, O'Neill had to abandon central Ulster and was followed by thousands of refugees, fleeing the revenge of the Scottish soldiers who inflicted terrible attacks on Irish civilians, persuaded by Protestant propaganda alleging atrocities against Anglo-Scottish settlers in the rebellion of 1641. To O'Neill, the devastation of Ulster made it look, "not only like a desert, but like hell, if hell could exist on earth". O'Neill stopped the killings of Protestant civilians, for which he received the gratitude of many Protestant settlers. From 1642 to 1646, a stalemate existed in Ulster, which O'Neill used to train and discipline his Ulster Army. This poorly supplied force nevertheless gained a bad reputation for plundering and robbing friendly civilians around its quarters in northern Leinster and southern Ulster. == Campaigns of 1643-45 ==