The Irish Rebellion of 1641 began as an attempted coup d'état by Irish Catholic gentry, but developed into inter communal violence between native Irish and English and Scottish Protestant settlers, starting a conflict known as the Irish Confederate Wars.
The rising was sparked by Catholic fears of an impending invasion of Ireland by anti-Catholic forces of the English Long Parliament and the Scottish Covenanters. In turn, the rebels' suspected association with the King of England, Scotland and Ireland, Charles I, exacerbated the situation leading up to, and ultimately resulting in, the start of the English Civil War. The Irish rebellion broke out in October 1641 and was followed by several months of violent chaos in Ireland before the Irish Catholic upper classes and clergy formed the Catholic Confederation in the summer of 1642. The Confederation became a de facto government of most of Ireland, free from the control of the English State and loosely aligned with the Royalist side in the Wars of the Three Kingdoms. The subsequent war continued in Ireland until the 1650s, when Oliver Cromwell's New Model Army decisively defeated the Irish Catholics and Royalists and re-conquered the country.
The roots of the 1641 rebellion lie in the failure of the English State in Ireland to assimilate the native Irish elite in the wake of the Elizabethan conquest and plantation of the country. The pre-Elizabethan Irish population is usually divided into the "Old (or Gaelic) Irish", and the Old English, or descendants of medieval Norman settlers. These groups were historically antagonistic, with English settled areas such as the Pale around Dublin, south Wexford, and other walled towns being fortified against the rural Gaelic clans. However, by the seventeenth century, the cultural divide between these groups, especially at elite social levels, was declining. Many Old English lords not only spoke the Irish language, but extensively patronised Irish poetry and music, and were described as Hiberniores Hibernis ipsis (more Irish than the Irish themselves). Intermarriage was also common. Moreover, in the wake of the Elizabethan conquest, the native population became defined by their shared religion, Roman Catholicism, in distinction to the new Church of England and Church of Scotland of settlers, and the officially Protestant (Church of Ireland) English administration in Ireland. During the decades in between the end of the Elizabethan wars of re-conquest in 1603 and the outbreak of rebellion in 1641, the political position of the wealthier landed Irish Catholics were increasingly threatened by the English government of Ireland.
The 16th and early 17th century English conquest of Ireland was marked by large scale "Plantations", notably in Ulster and Munster. These were mass dispossessions of Irish landowners who had rebelled against the crown, and sometimes their workers, and the granting of their land to colonists from England and Scotland. The terms of the Plantation, particularly in Ulster, were very harsh on the native population, who were forbidden from owning or renting land in planted areas and also from working there on land owned by settlers. The main reason for this was the dispossession of formerly powerful Irish clan leaders, such as the O'Neills and the O'Donnells, who fled the country in the Flight of the Earls in 1607. Other Catholic lords, such as the Magennis clan in County Down, sold much of their land to new settlers by the 1630s. The only sizeable plantation of confiscated land after 1630 was a part of the O'Byrne lands in County Wicklow.
Many of the exiles (notably Owen Roe O'Neill) found service as mercenaries in the Catholic armies of Spain and France. They formed a small émigré Irish community, militantly hostile to the English-run and Protestant state in Ireland, but restrained by the generally good relations between England and Spain and France after 1604. In Ireland itself, though the resentment caused by the plantations was one of the principal causes for the outbreak and spread of the rebellion in 1641, 80% of freehold land still belonged to Catholics.
Most of the Irish Catholic upper classes were not ideologically opposed to the sovereignty of the Charles I over Ireland, but wanted to be full subjects of the triple monarchy (England, Scotland, and Ireland) and maintain their pre-eminent position in Irish society. This was prevented by two factors, firstly their religious dissidence, and secondly the threat posed to them by the extension of the Plantations. The failed Gunpowder Plot of 1605 curtailed the rights of wealthy Irish Catholics, and unfairly so as they had not been involved. Protestantism was the only approved form of worship of the Three Kingdoms. Non-attendance at Protestant church services was punishable by "recusant fines" and the public practice of unapproved faiths by arrest. Catholics could not hold senior offices of state, or serve above a certain rank in the army. The Irish privy council was dominated by the Protestant Ascendancy. The constituencies of the Irish House of Commons were re-arranged so as to give Protestants a majority in it by the session of 1613. Moreover, the Irish Parliament was subordinate to the English Parliament by a 15th century ordinance known as Poynings' Law. The Protestant Ascendency (and therefore settler) dominated administration took opportunities to confiscate more land from longstanding landowners by questioning their land titles.
In response, Irish Catholics sought what were called The Graces, and appealed directly to the King, first James I and then Charles I, for full rights as subjects and toleration of their religion. On several occasions, the Monarchs appeared to have reached an agreement with them, granting their demands in return for raising taxes. However, Irish Catholics were disappointed when, on paying the increased levies after 1630, Charles postponed the implementation of their demands. What was more, by the late 1630s, Thomas Wentworth, Charles’ representative in Ireland, launched a new round of plantations, though these had not been effected by 1641. On the pretext of checking of land titles to raise revenue, Wentworth confiscated and was going to plant lands in Roscommon and Sligo and was planning further plantations in Galway and Kilkenny directed mainly at the "Old English" families. In the judgement of historian Padraig Lenihan, 'It is likely that he [Wentworth] would have eventually encountered armed resistance from Catholic landowners' if he had pursued these policies further. However the actual rebellion followed the destabilisation of English and Scottish politics and the weakened position of the king in 1640.
In 1638 to 1640 many Scots rose in a revolt known as the Bishops' Wars against Charles I's attempt to impose Church of England prayers there, believing them to be too close to Catholicism. The King's attempts to put down the rebellion failed when the English Long Parliament, which had similar religious concerns to the Scots, refused to vote in 1641 for new taxes to pay for raising an army. Charles therefore started negotiations with Irish Catholic gentry to recruit an Irish army to put down the rebellion in Scotland, in return for the concession of Irish Catholics' longstanding requests to practise their religion openly. To the Scots and the English Parliaments, this appeared to confirm that Charles was a tyrant, who wanted to impose Catholicism on his kingdoms, and to govern again without reference to his Parliaments as he had done in 1628–1640. During the early part of 1641, some Scots and Parliamentarians even proposed invading Ireland and subduing organized Catholicism there, to ensure that no royalist Irish Catholic army would land in England.
Frightened by this, and wanting to seize the opportunity, a small group of Irish Catholic landowners conceived a plan to take Dublin Castle and to control other important towns around the country in a quick coup in the name of the King, both to forestall a possible invasion and to force him to concede the Catholics' demands. More importantly, Charles had failed to beat the Scots, his ministers were under pressure from the "Short" and "Long" London parliaments in 1640–41, and this apparent weakness made it much more likely that a rebellion would be successful.
Economics also contributed to the outbreak of the rebellion. Interest rates in the 1630s had been as high as 30% per annum. The Irish economy had hit a recession and the harvest of 1641 was poor. The leaders of the rebellion like Phelim O'Neill and Rory O'Moore were heavily in debt and risked losing their lands to creditors. What was more, the Irish peasantry were hard hit by the bad harvest and were faced with rising rents. This aggravated their desire to remove the settlers and contributed to the widespread attacks on them at the start of the rebellion.
The planners of the rebellion were a small group of Irish landowners, mainly Gaelic Irish and from the heavily planted province of Ulster. Hugh MacMahon and Conor Maguire were to seize Dublin Castle, while Phelim O’Neill and Rory O’Moore were to take Derry and other northern towns. The plan, to be executed on 23 October 1641, was to use surprise rather than military force to take their objectives and to then issue their demands, in expectation of support from the rest of the country. However, the plan for a fairly bloodless seizure of power was foiled when the authorities in Dublin heard of the plot from an informer (a Protestant convert named Owen O’Connolly) and arrested Maguire and MacMahon.
O'Neill meanwhile successfully took several forts in the north of the country, claiming to be acting in the King's name. Fairly quickly, events spiraled out of the control of the men who had instigated them. The English authorities in Dublin over-reacted to the rebellion, which they characterized as 'a most disloyal and detestable conspiracy intended by some evil affected Irish Papists' which they claimed was aimed at 'a general massacre of all English and Protestant inhabitants'. Their response was to send troops under commanders Charles Coote and William St Leger (themselves Protestant settlers) to rebel held areas in counties Wicklow and Cork respectively in early 1642. Their expeditions were characterised by what modern historian Padraig Lenihan has called, 'excessive and indiscriminate brutality' against the general Catholic population there and helped to provoke the general Catholic population into joining the rebellion.
Meanwhile, in Ulster, the breakdown of state authority prompted widespread attacks by the native Irish population on the English Protestant settlers. Initially, Scottish settlers were not attacked by the rebels but as the rebellion went on, they too became targets. Phelim O’Neill and the other insurgent leaders initially tried to stop the attacks on the settlers, but were unable to control the local peasantry. A contemporary - though hostile - Catholic source tells us that O'Neill "strove to contain the raskall multitude from those frequent savage actions of stripping and killing which were after perpetrated and gave their enterprise an odious character as well in the opinion of their countrymen as of strangers" but that "the floodgate of rapine, once being laid open, the meaner sort of people was not to be contained".
Communal uprisings spread to the rest of the country. Munster was the last region to witness such disturbances; the rebellion in Munster was in fact largely a product of the severe martial law William St Leger imposed upon the province. Many Irish Catholic lords who had lost lands or feared dispossession joined the rebellion and participated in the attacks on the settlers. However, at this stage, the attacks usually involved the beating and robbing rather than the killing of Protestants. Historian Nicholas Canny writes, 'most insurgents seemed anxious for a resolution of their immediate economic difficulties by seizing the property of any of the settlers. These popular attacks did not usually result in loss of life, nor was it the purpose of the insurgents to kill their victims. However they were always gruesome affairs because they involved face to face confrontations between people who had long known each other. A typical offensive involved a group of Irish descending upon a Protestant family and demanding, at knife point, that they surrender their moveable goods. Killings usually only occurred where Protestants resisted'.
The motivations for the popular rebellion were complex. Among them were a desire to reverse the plantations; rebels in Ulster were reported as saying, 'the land was theirs and lost by their fathers. Another motivating factor was a sharp antagonism towards the English language and culture which had been imposed on the country. For example, rebels in county Cavan forbade the use of the English language and decreed that the original Irish language place names should replace English ones. A third factor was religious antagonism. The rebels consciously identified themselves as Catholics and justified the rising as a defensive measure against the Protestant threat to 'extirpate the Catholic religion'. Rebels in county Cavan stated, "we rise for our religion. They hang our priests in England". Historian Brian MacCuarta writes, "Longstanding animosities against the [Protestant] clergy were based on the imposition of the state church since its inception thirty years previously. Ulster Irish ferocity against everything Protestant were fuelled by the wealth of the church in Ulster, exceptional in contemporary Ireland". There were also cases of purely religious violence, where native Irish Protestants were attacked and Catholic settlers joined the rebellion.
The number of planters killed in the early months of the uprising is the subject of debate. Early English Parliamentarian pamphlets claimed that over 200,000 settlers had lost their lives. In fact, recent research has suggested that the number is far more modest, in the region of 4,000 or so killed, though many thousands were expelled from their homes. It is estimated that up to 12,000 Protestants may have lost their lives in total, the majority dying of cold or disease after being expelled from their homes in the depths of winter. 
The general pattern around the country was that the attacks intensified the longer the rebellion went on. At first, there were beatings and robbing of local settlers, then house burnings and expulsions and finally killings, most of them concentrated in Ulster. Historian Nicholas Canny suggests that the violence escalated after a failed rebel assault on Lisnagarvey in November 1641, after which the settlers killed several hundred captured insurgents. Canny writes, 'the bloody mindedness of the settlers in taking revenge when they gained the upper hand in battle seems to have made such a deep impression on the insurgents that, as one deponent put it, "the slaughter of the English" could be dated from this encounter' In one incident after this battle, the planters in Portadown were taken captive and then killed on the bridge in the town (see the Portadown Massacre). In nearby Kilmore parish, English and Scottish men, women and children were burned to death in the cottage in which they were imprisoned., In County Armagh, recent research has shown that about 1,250 Protestants were killed in the early months of the rebellion, or about a quarter of the planter population there. In County Tyrone, modern research has identified three blackspots for the killing of settlers, with the worst being near Kinard, 'where most of the British families planted... were ultimately murdered' .
Modern historians have argued that the killings of 1641 had a powerful psychological impact on the Protestant settlers.  Dr. Mary O'Dowd, 'To look at the long-term consequences of the Plantation, it's very difficult to do that without also taking into consideration the long-term implications of the 1641 rebellion: because the massacres of 1641, in the winter of 1641, really were very traumatic for the Protestant settler community in Ulster, and they left long-term scars within that community.
Contemporary Protestant accounts depict the outbreak of the rebellion as a complete surprise, one stated that it was, 'conceived among us and yet we never felt it kick in the womb, nor struggle in the birth' . However after the rebellion, many Protestants in Ireland took the attitude that the native Irish could not be trusted to remain quiescent again. The Protestant narrative of the rebellion as a preconceived plot to massacre them was constructed in the Depositions, a collection of accounts by victims assembled between 1642 and 1655 and now housed in Trinity College Dublin and articulated in a book published by John Temple in 1642, entitled The Irish Rebellion .
Many settlers massacred Catholics when they got the chance, particularly in 1642–43 when a Scottish Covenanter army landed in Ulster. William Lecky, the 19th century historian of the rebellion, concluded that, "it is hard to know on which side the balance of cruelty rests".
Among the more prominent incidents was the killing of Irish prisoners at Kilwarlin woods near Newry and the subsequent massacre of Catholic prisoners and civilians in the town itself. Trevor Royle quotes James Turner who in his memoirs reported that after skirmish in Kilwarlin woods, Irish prisoners were given "bad quarter, being shot dead", but two other eye witness accounts of the skirmish, (a letter by Roger Pike and the dispatches of Major-General Robert Monro, the Protestant commander), do not mention the killing of prisoners. Turner records in his memoirs that the following day English soldiers entered Newry and captured its castle, after the capitulation Catholic soldiers and local merchants were lined up on the banks of the river and "butchered to death ... without any legal process".
On Rathlin Island Covenanter Campbell soldiers of the Argyll's Foot were encouraged by their commanding officer Sir Sir Duncan Campbell of Auchinbreck to kill the local Catholic MacDonalds, near relatives of their arch Clan enemy in the Scottish Highlands Clan MacDonald, this they did with ruthless efficiency throwing scores of MacDonald women over cliffs to their deaths on rocks below. The number of victims of this massacre has been put as low as 100 and as high as 3,000.
The widespread killing of civilians was brought under control to some degree in 1642, when Owen Roe O'Neill arrived in Ulster to command the Irish Catholic forces and hanged several rebels for attacks on civilians. Thereafter, the war, though still brutal, was fought in line with the code of conduct that both O'Neill and the Scottish commander Robert Munro had learned as professional soldiers in continental Europe.
In the long term, the killings committed by both sides in 1641 intensified the sectarian animosity that originated in the plantations. The effects of this can still be seen, particularly in Northern Ireland, today. The bitterness created by the plantations and the massacres of 1641 proved extremely long lasting. Ulster Protestants commemorated the anniversary of the rebellion on every 23 October for over two hundred years after the event. According to Padraig Lenihan, 'This anniversary helped affirm communal solidarity and emphasize the need for unrelenting vigilance; [they perceived that] the masses of Irish Catholics surrounding them were and always would be, unregenerate and cruel enemies' Images of the massacres involving Protestant deaths in 1641 are still represented on the banners of the Orange Order. Even today, the killings are thought of by some as an example of attempted genocide . In fact, if the upper estimate of 12,000 deaths is accurate, this would represent less than 10% of the British settler population in Ireland, though in Ulster the ratio of deaths to the settler population would have been somewhat higher, namely around 30% .
see also: Confederate Ireland and Irish Confederate WarsFrom 1641 to early 1642, the fighting in Ireland was characterized by small bands, raised by local lords or among local people, attacking civilians of opposing ethnic and religious groups. At first, many of the Irish Catholic upper classes were reluctant to join the rebellion, especially the "Old English" community. However, within six months almost all of them had joined the rebellion. There were three main reasons for this.
By early 1642, there were four main concentrations of rebel forces; in Ulster under Phelim O'Neill, in the Pale around Dublin led by Viscount Gormanstown, in the south east, led by the Butler family - in particular Lord Mountgarret and in the south west, led by Donagh MacCarthy, Viscount Muskerry. In areas where British settlers were concentrated, around Cork, Dublin, Carrickfergus and Derry, they raised their own militia in self-defense and managed to hold off the rebel forces.
Charles I was initially hostile to the rebels and sent over a large army to Dublin to subdue them. The Scottish parliament also sent an army to Ulster to defend their compatriots there. However, a quick defeat of the rebels in Ireland was prevented by the outbreak of Civil War in England. Among other issues, the English Parliament did not trust Charles with command of the army raised to send to Ireland, fearing that it would afterwards be used against them. Because of the Civil War in England, English troops were withdrawn from Ireland and a military stalemate ensued.
This gave the Irish Catholics breathing space to create the Catholic Confederation, which would run the Irish war effort. This was instigated by the Catholic clergy and by landed magnates such as Viscount Gormanstown and Lord Mountgarret. By the summer of 1642, the rebellion proper was over and was superseded by a conventional war between the Irish, who controlled two thirds of the country, and the British-controlled enclaves in Ulster, Dublin and around Cork in Munster. The following period is known as Confederate Ireland. The Confederation sided with the Royalists in return for the promise of self-government and full rights for Catholics after the war. They were finally defeated by regiments of the English Parliament's New Model Army from 1649 through to 1653 and land ownership in Ireland passed almost exclusively to Protestant settlers.