Historian Aidan Clarke writes that religion "was merely one aspect of a larger problem posed by the Gaelic Irish, and its importance was easily obscured; but religious difference was central to the relationship between the government and the colonists".

[1] During the decades between the end of the Elizabethan wars in 1603 and the outbreak of rebellion in 1641, the political position of the wealthier landed Irish Catholics was increasingly threatened by the English government of Ireland.

They formed a small émigré Irish community, militantly hostile to the English-run Protestant state in Ireland, but restrained by the generally good relations England had with Spain and France after 1604.

Both they and the majority Catholic population were required to pay tithes to the church, causing great resentment, while practicing Catholicism in public could lead to arrest, and non-attendance at Protestant service was punishable by recusant fines.

[12] In response, the Irish Catholic upper classes sought 'The Graces', and appealed directly first to James I and then his son Charles, for full rights as subjects and toleration of their religion.

However, despite paying increased taxes after 1630, Charles postponed implementing their demands until 3 May 1641 when he and the English Privy Council instructed the Lords Justices of Ireland to publish the required Bills.

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 for new taxes to pay for raising an army.

Due to take place on Saturday 23 October 1641,[c] armed men led by Connor Maguire and Rory O'Moore were to seize Dublin Castle and its arsenal, then hold it until help came from insurgents in neighbouring County Wicklow.

[23] The plan to seize Dublin Castle was foiled when one of the ringleaders, Hugh Og MacMahon, revealed details to his foster-brother, a Protestant convert named Owen O'Connolly.

The suspension of the Irish Parliament on 17 November deprived them of the political means to resolve these issues and the declaration provided cover for moderates such as Nicholas Plunkett to make common cause with the rebels.

[30] Rumours also circulated that radical Protestants were seeking to replace Charles I with his exiled German nephew the Elector Palatine, paving the way for increased repression of Irish Catholics.

[35] This setback and the stubbornness displayed by the town's defenders allegedly made a deep impression on the attackers, since it showed hopes of a quick and relatively painless victory in Ulster were over optimistic.

[38] In December, troops led by Charles Coote, Governor of Dublin Castle, and William St Leger, Lord President of Munster, attacked rebel-held areas in counties Wicklow and Tipperary respectively, expeditions characterised by "excessive and indiscriminate brutality" against the general Catholic population.

[41] The situation changed when it became clear the rising had been only partially successful, while the breakdown of state authority prompted widespread attacks by the Catholic peasantry on Protestants, regardless of nationality.

[45] They intensified as the rebellion progressed, particularly in Ulster where many had lost land in the post 1607 Plantations,[46] while attacks on local Protestant clergy were in part due to resentment at the relative wealth of the Church of Ireland in that province.

[50] In nearby Kilmore, English and Scottish men, women and children were burned to death in the cottage in which they were imprisoned, while in Armagh as a whole, some 1,250 died in the early months of the rebellion, roughly a quarter of the local settler population.

[53] The arrival of a Covenanter army in Ulster in April 1642 led to further such atrocities, William Lecky, a 19th-century historian of the rebellion, concluding "it is far from clear on which side the balance of cruelty rests".

[55] The killings were brought under some degree of control by Owen Roe O'Neill, who in July 1642 was given command of Irish forces in Ulster and hanged several rebels for attacking civilians.

[60] They were used to support the view of the rebellion as a Catholic conspiracy to wipe out all Protestants in Ireland,[61] a narrative constructed in the Depositions, a collection of victim reports gathered between 1642 and 1655 and now housed in Trinity College Dublin.

[65] In the long term, the 1641 massacres intensified existing sectarian animosity on both sides, although modern historians argue the killings had an especially powerful psychological impact on the Protestant community.

According to historian Pádraig Lenihan, this "helped affirm communal solidarity and emphasise the need for unrelenting vigilance [against] the masses of Irish Catholics surrounding them [who] were and always would be, unregenerate and cruel enemies".

[g] On 4 November, Parliament voted to send weapons and gunpowder to Ireland and recruit 8,000 men to suppress the rising but the situation was complicated since any such army would be legally controlled by the king.

[71] A series of alleged Royalist military conspiracies in 1641 and rebel claims that Charles supported their actions heightened fears he would turn it against his opponents in England and Scotland, rather than the Irish.

[72] The Covenanters urged the English Parliament to fund a Scottish army rather than recruiting their own, arguing it could reach Ireland more easily and would be independent of both Charles and his Parliamentary opponents.

[74] James Butler, 1st Duke of Ormond, a member of one of the leading Old English families and Protestant convert, was made commander of Royal forces in Ireland and recruited three infantry regiments from the refugees flooding into Dublin.

[75] Many politicians and officials in Dublin and London opposed Scottish intervention in Ulster, seeing a well-armed and independent Presbyterian army as a threat to the status quo, and Parliament continued recruiting English regiments.

[76] On 21 December, the Lords approved a Scottish army of 10,000 but the Covenanter government insisted they should also be given control of the three largest ports in Ulster, Carrickfergus, Coleraine and Derry, along with land grants.

[27] By mid-1642, Protestant forces in Ireland totalled 40,000 infantry and 3,600 horse, [80] but the outbreak of the First English Civil War in August 1642 ended the flow of reinforcements and money from England and a military stalemate ensued.

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.

Hugh O'Reilly (archbishop of Armagh) held a synod of Irish bishops at Kells, County Meath on 22 March 1642, which legitimised the rebellion as war in defence of the catholic religion.