Rebellion & Confederacy
Overview
The period from 1640 to 1653 represents one of the most turbulent periods in Irish history. The so-called wars of the three kingdoms were a complex set of interrelated events involving the crown, Parliament and various interests in Ireland.
They involved several wars, including the first, second and third English Civil War and other distinct wars with different protagonists in succession with changing of sides by key players. The ultimate result in Ireland was the utter devastation of much of the countryside. It broke the power of the surviving, most of the surviving old English and Gaelic lords.
Charles I and Parliament
Charles I policies of monarchical rule had led him into conflict with Parliament in England. The Lord Deputyship of Wentworth in Ireland had gone very far in achieving royal absolutism.
In Scotland, the national covenant was subscribed to by many Scots, promising resistance to the King’s effort to impose English religious forms and structures. To counter this, Wentworth in Ireland compelled all males over 16 to swear a black oath of loyalty to the King.
As the King’s fortunes waned and he fell into conflict with parliament, Wentworth’s control of Ireland had been so thoroughly established that he was in a position to raise an army on the King’s behalf in Ireland maintained by the Irish Parliament, under the command of the Earl of Ormond. Although he was a Protestant, it was largely manned by Catholic troops. The Army was disbanded after Wentworth’s execution in 1641 at the behest of Parliament and with the ready assistance of the many enemies Wentworth had made in Ireland.
As Charles came into conflict with parliament, control of the administration was in the hands of two Lord Justices appointed by the King but with pro-Parliament sympathies. Many in Ulster supported the alliance between the Scots and the English Parliamentarians. New English, mainly Anglicans but often with puritan sympathies, tended to support the parliamentary side.
The  old English although they mistrusted the King,  had little choice to support him due to the evident threat from the puritanical zeal of the parliamentarians. It appeared to some that a royalist Catholic Ireland could be established under the King who continued to seek support from Earls of Antrim and Ormond in 1641.
Confederation of Kilkenny
At the same time former Gaelic chiefs, together with leading Irish abroad sought a revolt to seize control of Ireland. An uprising commenced in Leinster and Ulster. Extensive massacre, burning and looting followed particularly in Ulster where many who had been dispossessed in the previous decade sought to fight a war to recover their positions. They were undoubted atrocities against civilians, although it appears the numbers were wildly exaggerated in reports in England.
The leader of the insurgents in Ulster, Sir Phelim O’Neill claimed to act on behalf of the King, which although disowned by the King did little to assist his weakening position with the Parliament. In Leinster  Chief Rory O’Moore achieved a victory over a small government force in November 1641. Ormond was appointed in charge of the Army.
By the end of the year, the Old English however were fighting for a royal, loyal Catholic Ireland with the Gaelic chiefs, ironically at this stage against both the King and Parliament. There was a breakdown between the new English settlers and the old English.
The uprising became nationwide and the rebels gained control of most of the country. In 1642 a proposal was made to form a provisional government in the King’s name and an assembly of clergy and lay leaders. The lords and gentry of the confederate Catholics met in Kilkenny. A supreme council and assembly was nominated. The confederate army was led by experienced soldiers with experience in continental European wars.
The King and the Confederates
By this time, the parliamentarians in England were at war with the King’s supporters. In mid-1642 Ormond and the King’s army led by Munro fought separately against the Confederates. In September 1643 after two years of indecisive military action, a truce was agreed between the Confederates and the King represented by Ormond, who was Lord Lieutenant.
The King was in communication with the confederates. The confederates demanded concessions before agreeing alliance with the King. The King was reluctant to water down his supremacy and discussions dragged on for two years.  They wished to do away with Ponying’s law and the King was requested to confirm the independence of the Irish Parliament. In the meantime, the English Parliament had passed the Adventurers Act.
A papal envoy Rinnucini was sent to Ireland, bringing a supply of arms and monies for the Confederate cause. A draft treaty between Ormond and the confederates was dismissed and its supporters threatened with ex-communication,  as it did not do enough to restore the rights of the Catholic church. O’Neill defeated a Scots army at Benburb and put his army at the disposal of the papal nuncio who took control of the confederate council.
Ormond and the Royalists
In 1647 negotiations resumed with the King through Ormond who still held Dublin. He was sceptical of obtaining terms that would satisfy the nuncio and he sought to negotiate with the Parliament to take over Dublin. By 1647 his forces had surrendered to parliamentary forces and he left the country under the command of a parliamentary officer.
Internal rivalries within the confederates soon weakened it. Lord Inchquin a protestant member of a Catholic family was fighting for the parliamentary cause in Munster. However, he switched loyalties to the King in 1848 and turned on his own former supporters,  who did not follow. By this stage, much of Munster was devastated by the fighting.
In 1649 the confederates, Inchquin and the King’s party entered an alliance with Ormond as the leader. However, by this time Parliament had prevailed over Charles I and executed him. The royalists in Ireland declared his son Charles II his heir and King.
The Confederation was dissolved, and the King’s government was entrusted to 12 commissioners under Ormond. The royalist army took Dundalk and Drogheda from parliamentary forces. Ormond’s attack on Dublin was stopped by a parliamentary victory in the battle of Rathmines.
Cromwell and Parliamentary Victory
In August 1649 Oliver Cromwell landed with 3,000 troops of his new model army with cannon and changed the balance of power decisively. He was determined to ensure Ireland will be pacified and placed under parliamentary control.
Drogheda was retaken from the royalists and much of the surrendered garrison was massacred. Similarly, Wexford and Kilkenny were captured.Cromwell left in 1650, leaving his son in law Ireton to complete the process of taking control of Ireland.
Charles II made a military deal with Presbyterian Scots to ensure their support and promised to enforce anti-Catholic legislation. Ultimately Ireton and his successors through a succession of sieges took on and captured the remaining fortified towns, securing the surrender of the royalist forces in 1652.
Conquest and the Restoration
The Cromwellian conquest completed the colonisation of Ireland, which became part of the  Commonwealth of England, Scotland and Ireland in 1653–59. It destroyed the native Irish Catholic land-owning classes and replaced them with colonists with a British identity
After the  Restoration in 1660, Charles II of England restored about a third of the confiscated land to the former landlords in the Act of Settlement 1662, but not all, as he needed political support from former parliamentarians in England.
Many of the Irish Catholic landed class tried to reverse the remaining Cromwellian settlement in the Williamite War in Ireland (1689–91), where they fought for the Jacobites. They were defeated once again, and many lost land that had been regranted after 1662.