Inclined to dispute the claim of his father's younger, legitimate brother Gerald FitzGerald, 14th Earl of Desmond, the current of politics proved too strong against James FitzThomas.
When of an age to understand his position as heir to a contested title, James Fitzthomas repaired to court to petition Elizabeth for a restoration of his rights.
Their petitions, however, no longer found favour at Elizabeth's court, for Munster was to be denuded of its native population, "planted" with Englishmen, and re-established as a settlement colony of England.
[3][4][5][6] In 1598, instigated by his brother John FitzThomas, and by Hugh O'Neill, Earl of Tyrone, Munster, in the words of the Irish annalists, again became "a trembling sod.
On 12 October 1598, realizing that he would obtain little if any justice, "to maintain his right, trusting in the Almighty to further the same," James FitzThomas stated both his grievances and intentions in response to the expostulations of the Earl of Ormond.
Dismissing his followers, the earl took to the woods for safety, where, in May 1601, Sir George Carew was informed that he was living "in the habit of a priest," but determined "to die rather than to depart the province, retaining still his traitorly hopes to be relieved out of Ulster or out of Spain.
"[8] Carew made several attempts to procure his capture or death, but without success, for "such is the superstitious folly of these people, as for no price he may be had, holding the same to be so heinous as no priest will give them absolution.
FitzGerald was placed in irons to prevent a rescue, "so exceedingly beloved of all sorts" was he, and conveyed to Shandon Castle, where he was immediately arraigned and adjudged guilty of treason.
Of his life in prison there remains only the following notice: "The demands of Sir John Peyton, Lieutenant of Her Majesty's Tower of London, for one quarter of a year, from St. Michael's day 1602 till the feast of our Lord God next.