His nephew by his only sister was Donough McCarthy, Viscount Muskerry, the most powerful confederate Catholic in Munster who later led the siege of Bunratty.

Meanwhile, the Confederate Catholic council at Kilkenny were assembling troops to be sent to England as part of a deal to assist King Charles I or perhaps to be used against the Protestants of Munster.

According to a letter written by the Parliamentarian Lord Broghill "the progress of our designes in the River of Lymerick hat not only diverted a supply of six thousand from going to the King, and ready to be shipped at Waterford, but also ruined their projects upon us."

Proof of the expedition being a diversionary tactic can be found in the Memorials of William Penn: "Having dined with his lordship we held consultation... to see whether he would join with us in the assaulting of the rebels in those parts, or at least the weakening and disabling them in their intentions upon the Lord of Inchiquin's quarters; or to obstruct the transportation of such forces... for the assistance of his majesty in this un-natural war against his subjects.

According to the Earl of Castlehaven's memoirs - "Lord Inchiquin, towards the Spring, sent along by sea from Cork 500 foot and 150 horsemen with saddles and all sorts of arms for horse and foot; who entering the Shannon, seized Bonratty in the county of Clare, a castle belonging to the Earl of Thomond, where they found a brave stable of horses and mares, on which he mounted all his horsemen.

[citation needed] Around this time, 6,000 men had been assembled by the Confederate Catholics and were waiting in Cashel and Clonmel before transport to Britain as part of a deal with the Royalists to serve the King but when this plan was seen as unfeasible, it was instead decided to send 300 as bodyguards to Charles, then Prince of Wales, in Jersey, and the rest were given over to the Earl of Glamorgan in order to take Bunratty, and if possible to attack Inchiquin.

According to Richard Belling's account from the point of the Confederates: The Lord of Muskery, having by his presence appeased the manie discontents of the souldiers and officers of the Mounster list, and composed them to a bodie, being now furnished with some money…..advanced to camp in the park of Bunratty, having taken a castle at the entrance into the parke….

On 23 June, an English sally repulsed according to Penn: "I had notice of a sally made by our men upon the enemy; but being much engaged, and not able to make retreat, after some execution done upon the rogues, had near on thirty of our men killed and wounded..." According to Meehan's account: "Sir Charles Coote falling with a strong body of the Laggan forces in to the counties of Roscommon and Galway, as was supposed with a design to penetrate into Thomond, and relieve Bonratty...

But fearing that the attempt might fail, the parliamentarian general contented himself with burning the crops about Portumna and Loughrea, and then returned to his quarters with large preys of corn and cattle.

This lasted four or five days till at length my Lord Inchiquin finding the check hindered him from destroying the country, retired to his garrisons, and I went to the siege.

"Fearing that the siege of Bunratty would be abandoned by the troops owing to their want of pay, I have come to the camp and brought all the money I had left and some of my own also to lend to them, and I will not leave the place until I see a certainty of success or else that victory is despaired of.

By 12 July the English fleet was forced to leave the vicinity of the castle because the Irish guns were now firing from the shore and doing major damage.

Gibbon...came on board... to give notice of the present condition of the garrison; that they had not above 300 serviceable men among them, the rest being killed or miamed, and so not be able to make any longer resistance, but must be constrained to make their conditions... these most perfidious rogues made divers shot at our shipping, shot one of them through and through... they plied us so hard with two guns at a time that we were forced to let slip; in this condition riding within musquet shot of the shore and expecting to be galled by the enemy's guns... being conceived impossible for us to continue or riding here that with what speed might be, the ships should weigh, and fall down so low that they might not lie within the command of the rebel's guns... nor could we well do so, the fort, without the shipping, not being able to subsist.

"The conditions are so mean, and so far beneath the honour of a soldier, that I should never have consented thereunto"[10] According to Richard Bellings' account: "they were content to capitulate for their lives only and the officers their swordes, leaving cannon, horses, arms ammunition, and provisions to the Confederates".