In July 1649 The Earl of Ormonde marched a combined force of English Royalists and Irish Confederates on Dublin, the last major foothold of parliamentary forces in Ireland. Ironically Ormonde himself had held Dublin two years prior when it was besieged by Irish Confederates, before abandoning it to English parliamentary forces.
The Confederate/Royalist coalition had been forged in blood, the years since the Irish Rebellion in 1641 had been years of bloody and ruthless wars. Even as a peace agreement had been reached in 1648, after a series of defeats for the confederates at the hands of parliamentarian forces, fighting continued against those catholics who could not stomach submitting to the protestants who had inflicted massacres on catholics only a few years prior.
In 1649 things were going well for the coalition, the parliamentary forces received almost no support from England, where Cromwell had his hands full with the second English Civil War. At the end of July Ormonde had camped his troops at Rathmines near Dublin, with the intent to besiege the city. On the second of August his troops started fortifying the half-demolished castle of Baggotrath on the outskirts of Dublin. Michael Jones, the defender of Dublin, decided to move against this danger with an army of 5.000.
Although Ormond’s army had stood to arms for just such an eventuality Jones quickly captured Baggotrath, and turned towards the main Royalist camp. Although the royalist forces were thrown in disarray, they were able to fall back on a line formed by Lord Inchiquin’s infantry. Despite suffering heavy losses Ormonde was able to hold the line long enough for Lord Dillon to march against the parliamentarian rear.
Chaotic fighting raged on throughout the day, until at the start of the evening the remaining Parliamentarians forced themselves past Dillon’s battered forces and retired to Dublin.
The parliamentarians had inflicted heavy losses on the Royalists, but at the cost of most of their own force. Lord Inchiquin who had been stationed in Munster with three regiments of horse had marched North upon hearing the news, and linked up with Ormonde the next day. With Ormonde´s troops occupying the countryside and his artillery dominating the harbour, the siege of Dublin continued for another 6 weeks.
Cut off from England and with no remaining allies in Ireland Jones surrendered Dublin and was allowed to return to england with his troops, leaving behind most of their weaponry.
With no port open to him Cromwell called of his planned invasion of Ireland until spring. But the intended invasion of Ireland was overtaken by events, as the Scots proclaimed Charles II their king. The bulk of the New Model Army marched north against the Scots, leaving only a small army to invade Ireland and attempt to gain a foothold there.
Because the English navy still commanded the Irish sea parliamentarian forces could land unopposed near Drogheda. Needing to to take Drogheda before the Royalists could send reinforcements the walls were quickly broken by artillery and the city taken by assault.
The royalist garrison was massacred to a man, along with hundreds of civilians. The victory of parliament was short-lived as Ormonde marched the main royalist army against Drogheda, while Dillon marched troops from Dublin past Drogheda to block the parliamentarians from the north. With most defensible positions destroyed in the Parliamentarian attack the city was soon assaulted and it’s defenders given no quarter.
The massacre of Drogheda did much to strengthen Irish resolve. The defense of Ireland was strengthened by new fortifications in coastal towns and a reorganization of the Royalist army into three armies tasked with guarding Ireland against any invasion. Although English Royalists remained in command of these armies, with Ormonde in overall command, the Irish nobility was incorporated into the army as well.
Parliamentary propaganda tried to make the best of it’s failure to recapture Ireland by casting Charles II as “the Irish King”, hoping to fuel anti-Irish and anti-Catholic resentment in England, even though the monarch did not so much as set foot on Irish soil during these years.
Upon the restoration of the Monarchy in 1660 the Irish Confederacy was dissolved and the Irish Parliament instituted. The confederacy had achieved most of its goals, with self-government of Ireland assured and religious equality for Catholics (in Ireland) granted by Charles II.
In reality: Ormonde’s troops were routed at the battle of Rathmines and never really recovered. Cromwell was able to use Dublin as ann entry point to Ireland and marched quickly against other coastal towns, Drogheda was just the first of many massacres. In total the human cost of the conquest of Ireland is estimated at between 200.000 and 600,000 death (15-50% of the total population), another 50.000 Irish were taken to the West Indies as slave laborers. Ireland was effectively colonized by the English under Cromwell, Charles II restored only part of the lands taken by Cromwell leaving the Irish almost completely disenfranchised.