The natural leadership of the Munster Geraldines is imprisoned in the Tower of London, and the Earldom is in the hands of a soldier, James Fitzmaurice Fitzgerald, the "captain general" of the Desmond military.

Fitzmaurice has little stake in a new demilitarized order in Munster, which envisages the abolition of the Irish lords’ private armies.

A factor that draws wider support for Fitzmaurice is the prospect of land confiscations, which had been mooted by Sidney and Peter Carew, an English colonist.

This ensures Fitzmaurice the support of important clans, notably MacCarthy Mor, O'Sullivan Beare and O'Keefe and two prominent Butlers –brothers of the Earl.

Fitzmaurice himself had lost the land he had held at Kerricurrihy in County Cork, which had been leased instead to English colonists.

He is also a devout Catholic, influenced by the Counterreformation, which has made him see the Protestant Elizabethan governors as his enemies.

To discourage Sidney from going ahead with the Lord Presidency for Munster and to re-establish Desmond primacy over the Butlers, he plans a rebellion against the English presence in the south and against the Earl of Ormonde.

Fitzmaurice however has wider aims than simply the recovery of Fitzgerald supremacy within the context of the English Kingdom of Ireland.

Before the rebellion, he secretly sends Maurice MacGibbon, Catholic Archbishop of Cashel, to seek military aid from Phillip II of Spain.

Gilbert's actions in the south of Ireland play a significant part in the outbreak of the first of the Desmond Rebellions.

A kinsman of his, Sir Peter Carew (another Devonshire man), is pursuing a provocative, and somewhat far-fetched, claim to the inheritance of certain lands within the Butler territories in south Leinster.

The Earl of Ormonde, a bosom companion of the queen's from her troubled youth and head of that family, is absent in England, and the clash of his family's influence with the lawful authority of Carew's claim has created havoc.

Gilbert is eager to participate and, after Carew's seizure of the barony of Idrone (in modern County Carlow), he pushes westward with his forces across the river Blackwater in the summer of 1569 and joins his kinsman to defeat Sir Edmund Butler, a younger brother of the Earl's.

Violence spreads in confusion from Leinster and ...

...across the province of Munster, when Fitzmaurice launches his rebellion by attacking the English colony at Kerrycurihy south of Cork city in June 1569 before attacking Cork itself and those native lords who refuse to join the rebellion.

Fitzmaurice’s force of up to forty-five hundred men goes on in July to besiege Kilkenny, seat of the Earls of Ormonde.

Sidney in response mobilizes six hundred English troops, who march south from Dublin; another four hundred troops land by sea in Cork.

Gilbert is now created colonel and governor of Munster by Sidney and charged with the pursuit of Fitzmaurice (whom Gilbert considers "a silly wood-kerne").

The Geraldines are driven from Kilmallock, but return to lay siege to Gilbert, who repels their superior force in a sally, in which his horse is shot from under him and his buckler transfixed with a spear.

He shows courage in striking out into rebel territory, and ...

...manages to march unopposed through Kerry and Connello, taking thirty to forty castles without the aid of artillery.

Fitzmaurice's forces break up, as individual lords have to retire to defend their own territories.

Gilbert in particular is notorious for the terror tactics he employs, killing civilians at random.

During three weeks of Gilbert's campaign, all are treated without quarter and put to the sword, including women and children—which explains, perhaps, the swiftness with which so many castles are abandoned before his advance.

He is also said to have sent Captain Apsley into Kerry to inspire terror.

In order to cow local supporters of the rebels, he chooses to put on gruesome spectacles after a day's killing, ordering the decapitation of the scattered corpses so that the heads can be brought to his camp in the evening, where they are arranged in two parallel rows, making a pathway to the flaps of his tent, along which the supplicants would tread in the presence of their late fathers, brothers and sons.

The practice of decapitating slain enemies is common in Gaelic Ireland at this time, but its adoption by an English military commander marching under the banner of justice for the oppressed is remarkable.

Ormonde returns from England at this point, calls in his brothers, and mobilizes Gaelic Irish clans antagonistic to the Geraldines, which causes the Geraldine resistance to weaken.

One of the chief rebels had come in to the government and confessed his treason in December 1569, after which Gilbert receives his knighthood at the hands of Sidney in the midst of the ruined Fitzmaurice camp, reputedly amid heaps of slain gallowglass warriors.

Sidney and Gilbert have meanwhile forced Fitzmaurice into the mountains of Kerry, whence he launches hit and run attacks on the English and their allies.

Most of Fitzmaurice's allies have submitted to Sidney by 1570; the most important, Donal MacCarthy Mor, had surrendered in November 1569.

The guerrilla campaign drags on nevertheless.

Fitzmaurice, one month after Gilbert's return to England, retakes Kilmallock with one hundred and twenty foot, defeating the garrison and sacking the town for three days, leaving it "the abode of wolves"; ...