In 1558, the castle—now noted as one of the principal stongholds of Thomond—was taken by Thomas Radclyffe, the Lord-Lieutenant of Ireland from Donal O'Brien of Duagh, last King of Thomond (died 1579), and given to Donal's nephew, Connor O'Brien.
He succeeded to the title on the death of his father, on 10 December 1559, and during his minority was the ward of Thomas Ratcliffe, third earl of Sussex, for whom he conceived a great friendship.
The post was held by senior nobles such as Thomas Radcliffe.
He enjoyed the confidence of the English Crown and was on good terms with successive Deputies, Sir Edward Bellingham, Sir James Croft and Thomas Radclyffe, 3rd Earl of Sussex.
By way of retaliation the English, under the Earl of Sussex and Lord Scrope, destroyed his stronghold at Branxholme Castle.
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Attempts were made by Thomas Radclyffe, 3rd Earl of Sussex, Lord Lieutenant of Ireland, to expel the MacDonnells back to Scotland.
The castle was ransacked and burnt in 1558 by Thomas Radclyffe, 3rd Earl of Sussex, Lord Deputy of Ireland under orders of Queen Mary I of England in retaliation of James's involvement in Ireland against the English.