The main issues were whether Irish Catholics or British Protestants held most political power and owned most of the land, and whether Ireland would be a self-governing kingdom under Charles I or subordinate to the parliament in England.

Catholicism was repressed, most Catholic-owned land was confiscated, and tens of thousands of Irish rebels were sent to the Caribbean or Virginia as indentured servants or joined Catholic armies in Europe.

The ultimate winner, the English parliament, arranged for the mass confiscation of land owned by Irish Catholics as punishment for the rebellion and to pay for the war.

In areas where British settlers were concentrated, around Cork, Dublin, Carrickfergus and Derry, they raised their own militia in self-defence and managed to hold off the rebel forces.

Charles I wanted control of Ireland to mobilise its resources against his opponents in England and Scotland; the Scots and their English Parliamentary allies aimed to prevent this.

As a result, neither side would tolerate the autonomous Catholic state demanded by Irish leaders and both were committed to further land confiscations; enforcing the Adventurers' Act was the primary objective of the 1649 Cromwellian conquest.

[11] This resulted in the formation of Irish Confederacy, based at Kilkenny; by the end of 1642, it controlled two-thirds of Ireland, including the ports of Waterford and Wexford, through which they could receive aid from Catholic powers in Europe.

While supported by most Irish Catholics, especially the clergy, many co-religionists among the upper classes were Royalists by inclination, who feared losing their own lands if the plantation settlements were overturned.

This allowed Garret Barry, a returned Irish mercenary soldier, to capture Limerick in 1642, while the English garrison in Galway was forced to surrender by the townspeople in 1643.

They were assisted by divisions among their opponents, with some areas held by forces loyal to Parliament, others by the Royalist Duke of Ormonde and the Covenanters pursuing their own agenda around Carrickfergus.

The reality was an extremely complex mix of shifting loyalties; for various reasons, many Ulster Protestants regarded the Scots with hostility, as did some of their nominal allies in Parliament, including Cromwell.

These were funded by an extensive system of taxation, equipped with supplies from France, Spain and the Papacy and led by Irish professionals like Thomas Preston and Owen Roe O'Neill, who had served in the Spanish army.

However, they arguably squandered an opportunity to conquer all of Ireland by signing a truce or "Cessation of Arms" with the Royalists on 15 September 1643, then spending the next three years in abortive negotiations.

The bitterness it engendered is illustrated by a Parliamentary Ordinance of October 1644, which forbade 'giving of quarter to any Irishman or Papist born in Ireland who shall be taken in Hostility against the Parliament either upon the Sea or in England and Wales.

'[15] An offensive against Ulster in 1644 failed to make significant progress, while defeat at Marston Moor in July made it increasingly clear the English Royalists were losing the war; two weeks later, the Earl of Inchiquin defected to Parliament, giving them control of the ports of Cork, Kinsale and Youghal.

[16] In late 1644, the Confederates took Bandon but Inchiquin retained control of Cork; Preston captured Duncannon in January 1645, then besieged Youghal but lack of supplies forced him to abandon the siege in March 1645.

Outside of Ulster, the treatment of civilians was less harsh, although the "no-mans-land" in between Confederate and British held territory in Leinster and Munster was repeatedly raided and burned, with the result that it too became de-populated.

[18] On 30 July, however, it was proclaimed in Dublin by the Royalists that the Confederate Supreme Council had signed a peace treaty on 28 March 1646 with King Charles as represented by Ormonde.

The treaty was signed unbeknownst to the Confederate military commanders and without the participation of the leader of the Catholic clergy, Rinuccini, who had arrived in Ireland with money and arms as the Papal Nuncio nine months earlier.

Rinuccini and the Confederate military commanders also believed that there might be a chance for them to defeat the English in Ireland and take total control given the magnitude of their recent victories.

[18][19][20] Trying next to take control of Ireland, the Confederate armies commanded by O'Neill and Preston attempted to capture Dublin, Ormonde's Royalist garrison by siege.

Ormonde then turned to negotiations with the English Parliament and ultimately handed the city over to a Parliamentarian army commanded by Colonel Michael Jones on 19 June 1647.

Amid factional fighting within their ranks over this deal, the Confederates dissolved their association in 1648 and accepted Ormonde as the commander in chief of the Royalist coalition in Ireland.

During this divisive period the Confederates missed a second strategic chance to reorganise while their opponents were engaged in the Second English Civil War (1648–49), which was lost by their royalist allies.

The Confederate/Royalist coalition wasted valuable months fighting with Owen Roe O'Neill and other former Confederates instead of preparing to resist the impending Parliamentarian invasion of Ireland.

By 1651, the remaining Royalist/Irish forces were hemmed into an area west of the River Shannon, holding only the fortified cities of Limerick and Galway and an enclave in County Kerry, under Donagh MacCarthy, Viscount Muskerry.

These operated from rugged areas such as the Wicklow Mountains, looting supplies and attacking Parliamentary patrols, who responded with forced evictions and the destruction of crops.

The last organised Irish force surrendered in Cavan in April 1653 and given passage to France to either serve in the French army or with the English Royalist Court in exile.

This created a class of landless former farmers and dramatically altered patterns of Irish land holding, the percentage owned by Protestants increasing from 41% to 78% over the period 1641 to 1660.

The Parliamentarian Army gained a major foothold in Ireland for the first time in 1644, when Inchiquin's Cork-based Protestant force fell out with the Royalists over their ceasefire with the Confederates.