Outbreak
However, the plan to take Dublin was bungled by two conspirators, Maguire and MacMahon, who were captured by the authorities. O'Neill went ahead and started the rebellion in the north, capturing the important fort of Charlemont but quickly found that he could not control the Irish Catholic peasantry he had raised. These people, many of whom had been displaced during the Plantation of Ulster, began attacking the Scottish and English Protestant settlers with varying intensity over a period of 5 months. Being in command, O'Neill has been blamed for complicity or lack of oversight in these massacres, the detail of which is still a matter of contentious debate.
On 24 October 1641 O'Neill issued the Proclamation of Dungannon in which he claimed to have the King's authorisation to rise in defence of the Crown and the Catholic religion. On 4 November 1641 O'Neill repeated these claims in his proclamation alongside Rory Maguire at Newry and read out a commission from Charles I of England dated 1 October, commanding him to seize: "... all the forts, castles, and places, of strength and defence within the kingdom, except the places, persons, and estates of Our loyal and loving subjects the Scots; also to arrest and seize the goods, estates, and persons of all the English Protestants, within the said kingdom to Our use. And in your care and speedy performance of this Our will and pleasure We shall rely on your wonted duty and allegiance to Us which We shall accept and reward in due time." This gave O'Neill's forces the impression that they were acting within the law. Charles later denied having issued the commission.
In November O'Neill attacked Lisburn several times but failed to take it.
Like other rebel leaders, O'Neill had difficulty with the discipline of his troops, which was compounded by his comparative lack of social status. In an effort to improve this O'Neill planned to have himself declared Earl of Tyrone at the historic site of Tullyhogue.
Nalson, in his "History of the General Rebellion in Ireland", described O'Neill as: "Sir Phelemy Roe O Neill, captain-generall of all the rebels, and chieftain of the O Neills, O Hagans, O Quyns, O Mellans, O Hanlons, O Corrs, McCans, McCawells, Mac Enallyes, O Gormelys, and the rest of the Irish septs in the counties of Tyrone and Ardmagh."