In later years, the government councillor, Sir
Henry Wallop, voiced his resentment at the denial of these lands to the
Plantation of Munster, which was established after the
Second Desmond Rebellion and the attainder of
Gerald Fitzgerald, 15th Earl of Desmond. Fitzgibbon was regularly traduced by government officials, and his hereditary enemy Lord Roche accused him of complicity in the late rebellion. He found himself under pressure to display unquestioning loyalty to a crown that was unpopular amongst his followers, and he struggled in these trying circumstances. In 1584, he accompanied the lord deputy, Sir
John Perrot, on the government's campaign in Ulster against
Sorley Boy MacDonnell, and was commended for his valour after receiving a wound. In April 1587, after Perrot's departure for England, Fitzgibbon was arrested by the government; the advice of Sir Anthony St Leger, to make him, "
shorter by the length of his head" was not taken, and in 1589 he was released on heavy recognizances. On balance, he showed some skill in maintaining his loyalty over a long period and, during a visit to England in 1590, he won a grant-entail-male of the ancestral lands. In 1596 Fitzgibbon was appointed sheriff of
County Cork, in which office he fulfilled his duties satisfactorily. There were suspicions of his complicity with the rebel
Hugh O'Neill, during the
Nine Years war (1595-1603: see
Essex in Ireland), but he submitted unconditionally to Sir George Thornton in May 1600 and blamed his folly on his son John, who had joined the crown's enemies. The queen's secretary, Sir
Robert Cecil, advised the
President of Munster, Sir
George Carew to take good pledges of Fitzgibbon, "
for, it is said, you will be cozened by him at last". During this period he is said to have virtually obliterated the cathedral at
Lismore. Doubts about his loyalty were raised at the highest point of the war, when he failed to capture the Súgan
Earl of Desmond,
James FitzThomas FitzGerald, as the rebel nobleman passed through Fitzgibbon's territory in May 1601, but Carew was happy enough with his conduct after that. He did at last manage to capture the Súgan
Earl of Desmond in caves near Mitchelstown, and in reward
Elizabeth I carried out the full restoration, by an act of parliament, of his lands and lineage. == Stuart loyalty ==