From A Concise History of Ireland by P. W. Joyce
580. In England the parliament had triumphed. The death of the king caused somewhat of a counter-movement in Ireland; and the royalist cause was now—1649—sustained by the confederates, with Ormond the lord lieutenant, and Inchiquin—now again turned royalist—at their head, and by the Scots of Ulster. They proclaimed the prince of Wales king as Charles II.; and they were well pleased when, in February 1649, Prince Rupert on their side entered the harbour of Kinsale with sixteen frigates.
581. Rinuccini, seeing his mission a failure, returned to Rome in February 1649. O'Neill, the only great soldier now in Ireland, was at the head of a small army of old Irish; but the other confederate leaders kept him in the background through jealousy.
582. On the side of the parliament Jones still held Dublin, and Sir Charles Coote Derry. Inchiquin took from them Drogheda, Dundalk, Newry, and Trim. Ormond besieged Dublin, first encamping at Finglas and afterwards at Rathmines. He sent major-general Purcell on 25th of July to fortify the old castle of Bagot Rath near Rathmines. But colonel Jones sallied forth in the night and surprised not only Purcell but Ormond himself, and utterly routed the whole army (2nd of August 1649). This great disaster was caused by the bad generalship of Ormond.
583. Oliver Cromwell was appointed by Parliament lord lieutenant and commander of the forces in Ireland, and landed at Dublin 14th August, 1649, with 9,000 foot, 4,000 horse, military stores, and £20,000 in money, accompanied by his son-in-law Ireton as second in command. He issued a proclamation against plunder, ordering that all supplies taken from the natives should be paid for.
584. He first proceeded against Drogheda. It had been garrisoned by Ormond with 8,000 troops, chiefly English, under Sir Arthur Ashton. Cromwell began by battering down the steeple of St. Mary's church. Next day, the 10th September 1649, the cannonade continued, till towards evening two breaches were made. Two desperate attempts to enter were repulsed; but the third succeeded; and immediately, on Cromwell's order, the whole garrison, including the commander Sir Arthur Ashton, with many friars and townspeople, were massacred.
After this, Trim, Dundalk, Carlingford, Newry, and several other places in the North surrendered.
585. Cromwell returned to Dublin, and marching south, appeared before Wexford. It was well fortified and garrisoned with 3,000 men, under the command of David Sinnott. Cromwell began his cannonade on the 11th of October, and when some breaches had been made, Sinnott asked for a parley.
But meantime the commander of the strong castle just outside the walls treacherously delivered it up to Cromwell's troops. This enabled a party of the besiegers to get into the town and open the gates. The garrison retreated to the market place, where they found the townspeople congregated. Here they defended themselves in desperation for an hour, but were overpowered by numbers; and Cromwell's soldiers under his orders killed garrison and townspeople without distinction to the number of 2,000 (11th of October 1649).
586. The fate of Drogheda and Wexford struck the Irish with terror; and many towns now yielded on mere summons. New Ross was surrendered by Lord Taaffe; but Ireton failed in his attempt to take Duncannon. Cork, Youghal, Kinsale, and some other southern places were given up by their garrisons. Having failed to take Waterford, Cromwell marched to Dungarvan, which at once surrendered; after which he rested his troops for a month in mid-winter at Youghal.
587. At the end of January 1650 he set out to traverse Munster. Most towns he came to were given up; and where there was serious resistance he usually executed the garrison. Kilkenny, where the plague was raging, was yielded in March.
588. Clonmel was commanded by Hugh O'Neill, Owen Roe's cousin—Owen himself having died a few months before—and here, in the month of May, Cromwell met with the most determined resistance he had yet experienced, losing 2,500 of his men in the attack. But O'Neill having exhausted his ammunition, quietly withdrew during the night with his men to Waterford unknown to Cromwell; and the town surrendered on favourable terms.
589. In the North, Coote and Venables were almost equally successful, and captured town after town; and by this time the Parliamentarians had possession of the greater number of the fortresses of both North and South.
590. After the surrender of Clonmel, Cromwell, seeing the country virtually subdued, sailed for England on the 29th May 1650, leaving Ireton to finish the war. In August Preston surrendered Waterford.
591. While the confederates were loyally fighting for the young king Charles, who was at this time in Scotland, he, in order to gain the favour of the Scots, repudiated any agreement with the Irish, and declared himself against allowing them liberty to practise their religion.
592. The Irish distrusted both Ormond and Inchiquin, both of whom had mismanaged the war, and who were suspected of intriguing with the parliament; and Ormond, finding he had lost the confidence of the Catholics, sailed from Galway for St. Malo in December, leaving lord Clanrickard as his deputy.
593. Limerick, the most important place in possession of the royalists, was next to be attacked. It was commanded by Hugh O'Neill, the defender of Clonmel. By forcing the passage of the Shannon at O'Brien's Bridge, Ireton got at the Clare side of the city, which was now invested on both sides. Meantime lord Muskerry, coming from the south to its relief, was defeated by lord Broghill, and his troops scattered.
594. O'Neill defended the city with great bravery; but there was disunion, and he was not supported by the magistrates; and the plague was raging among the citizens. At length colonel Fennell betrayed his trust by opening the gates to Ireton, who took possession on the 27th of October 1651. The garrison of 2,500 laid down their arms and were allowed to march away unmolested.
Ireton caused several of the prominent defenders to be executed, among them Dr. O'Brien bishop of Emly; but he was himself killed by the plague within the same month. The traitor Fennell was hanged with the others, though for a different reason.
595. After Ireton's death, lieutenant-general Edmund Ludlow taking command, marched to the aid of Coote at Galway, which surrendered on the 12th May 1652, after a siege of nine months. The capture of a few detached castles completed the conquest of Ireland by the Parliamentarians.
596. Charles Fleetwood, Cromwell's son-in-law (he had married Ireton's widow) took command of the army in succession to Ludlow, and was afterwards appointed lord deputy. Under his direction a High Court of Justice was instituted in October 1652, to punish those who had been concerned in the rising of 1641; about 200 were sentenced and hanged, and among them Sir Phelim O'Neill.