Carew was instructed by Cecil to keep FitzGerald under close observation, ready to arrest him if he showed sympathy with the rebels while allowing the appearance of liberty.

FitzGerald's party set out from Bristol in October 1600, bound for Cork, but the prisoner suffered such a severe bout of sea-sickness that he had to be landed at Youghal in south Munster.

He was received enthusiastically by the Geraldine supporters – though the mayor of Cork was not courteous – and was quickly transferred to Mallow, and then to Kilmallock in the heart of Desmond country, where he was given lodgings by the English commander Sir George Thornton.

On his arrival he praised the queen's clemency and was well-liked; the next day – a Sunday – he ostentatiously made his way to the Protestant church, while his followers awaited him in the Catholic chapel, a disappointment for which he was instantly derided by the people.

In November 1600 the fortress of Castlemaine was surrendered to FitzGerald by a servant of the Súgán Earl, but owing to his failure to command the allegiance of the people the government soon discarded the Desmond heir.