The earliest Plantations of Ireland, which had occurred in the context of the Tudor reconquest of Ireland, had been intended to pacify and Anglicize the country under English rule and incorporate the native ruling classes into the English aristocracy.

Ireland was by this means to become a peaceful and reliable English possession, and would no longer be a source of rebellions and a potential base for foreign invasions.

"Plantations" or colonization, which play a major part in this policy, had taken two forms in the first half of the sixteenth century.

The first was "exemplary plantations", where small colonies of English settlers were installed to provide model farming communities that the Irish could emulate.

One such colony has been planted at Kerrycurihy, near Cork city in land leased off James FitzGerald, the 14th Earl of Desmond.

Desmond had in January 1541 agreed, as one of the terms of his submission to Henry VIII of England, to send Gerald FitzGerald, his eight-year-old son by his second wife More O'Carroll, to be educated in England.

Proposals to this effect had been renewed at the accession of Edward VI; Gerald was to be the companion of the young king.

Unfortunately for the subsequent peace of Munster, these projects have not been carried out.

The FitzGeralds hold the Desmond estates by a doubtful title, and the Butlers, the hereditary enemies of the Geraldines, make claims on them based on the marriage of James Butler, 9th Earl of Ormonde, to Lady Joan Fitzgerald, daughter and heiress-general of James FitzGerald, 10th Earl of Desmond.

On Ormonde's death in 1546, Lady Joan had proposed to marry Gerald FitzGerald, and eventually did so, after the death of her second husband, Sir Francis Bryan.

The effect of this marriage has been a temporary cessation of open hostility between the Desmonds and the eldest of Joan’s three sons by James, Thomas Butler, 10th Earl of Ormonde.

The second category of Irish plantation, and one which is to set the trend for future English policy in Ireland, is punitive plantations; in other words, confiscation of lands for rebellion and granting them to English settlers.

The first such scheme is the Plantation of the midlands counties of Laois and Offaly in 1556.

The O’Moore and O’Connor clans that occupy the area had traditionally raided the English-ruled Pale around Dublin.

At the death of Brian mac Cathaoir O Conchobhair Failghehe, the last de facto king of the ancient Kingdom of Uí Failgh (Offaly), the region of the present Irish county of Offaly in Leinster province, the Lord Deputy of Ireland, the Earl of Sussex, orders that they be dispossessed and replaced with an English settlement.

Laois is renamed Queen's County and Offaly shired into King's County, named after the new monarchs.

The county town is Daingean, the former stronghold of the O'Connor Faly dynasty, and renamed—briefly—Philipstown; ...

…the county town of Queen's County is a fort named Maryborough (present Portlaoghise).

The plantation is not a great success.

The O’Moores and O’Connors retreat to the hills and bogs and for much of the following forty years will wage a local war against the settlement.

English colonists will be settled during Mary's reign in the Irish Midlands to reduce the attacks on the Pale (the colony around Dublin).

The term Old English (Irish: Seanghaill), coined in the late sixteenth century and retrospectively applied to the descendants of the settlers who came to Ireland from Wales, Normandy and England after the twelfth century conquest of the country, is designed to describe the section of the above community which lives within the heart of English rule in Ireland, The Pale.

Many of the Old English have become assimilated into Irish society over the centuries and their nobility had effectively been the ruling class in the land up to the sixteenth century.

The south of Ireland (the provinces of Munster and southern Leinster) is dominated, as it has been for over two centuries, by the Old English Butlers of Ormonde and Fitzgeralds of Desmond, who form what are essentially miniature feudal principates.

Both houses raise their own armed forces and impose their own law, a mixture of Irish and English customs independent of the English government of Ireland in Dublin.

Successive English administrations in Ireland have been trying since the 1530s to expand English control over all of Ireland.

In the absence of any strong central government in Munster, the two rival dynasties remain locked in a cycle of violent competition.

The Fitzgerald territory is located in the south and southwest of Ireland, across modern counties; Cork, Kerry and Tipperary.

The Ormonde territory is centered on the city of Kilkenny and concentrated in counties Kilkenny, Waterford and Tipperary.

Both territories have experienced constant raiding as each side has tried to consolidate and expand its territory at the expense of the other.

The widowed Countess of Ormonde, mother of Sir Thomas Butler, 10th Earl of Ormonde, had married Gerald Fitzgerald, 15th Earl of Desmond, with a view to reconciliation between the two houses, and it had been to her intervention that the peaceful outcome of a standoff at Bohermore (known as the battle that never was) in 1560 was attributed.

Her death in 1564 unleashes ill feeling, however,and raiding is presently resumed on both sides.

Sir Maurice Fitzgerald—a Desmond dependent resident in the borderland between the territories—had during the ebb and flow of the dispute between the Butlers and the Fitzgeralds declared his intention to accept the protection of his first cousin, Thomas Butler, Earl of Ormonde, 

Gerald Fitzgerald, Earl of Desmond, musters the Geraldine forces in January 1565 in order to coerce him back into dependency, and marches east across Munster and into the territory of the Decies in Waterford.

Ormonde mobilizes his men to intercept the Geraldines at Affane, a ford over the Finisk tributary of the Blackwater River, in the foothills of the Knockmealdown Mountains near Lismore.

Here, the rival forces fight a pitched battle against each other in a blatant defiance of the Elizabethan state's law.

After Desmond is wounded and thrown from his horse, the Geraldine troops are routed and pursued by the Butlers to the riverbank.

About three hundred Geraldines are killed, with many drowning as they are intercepted by armed boats in crossing the river.

Desmond is taken in captivity to Clonmel and then to Waterford city, where Lord Justice Arnold takes custody of him after a legal wrangle with Ormonde.

A furious Elizabeth I summons the heads of both houses to London to explain their actions.

The fact that both sides had displayed their banners in the battle was a particular affront to her—as it had been a symbolic rejection of the monopoly of the state on making war.

However, the treatment of the dynasties is not even handed.

Ormonde—who, as a cousin of the Queen's and a court favorite, manages to persuade Elizabeth that it is the Geraldines who are at fault—is pardoned.

Desmond (who had been brought before the privy council on a litter) and his brothers, John and James, are on Ormonde’s urging arrested and detained in the Tower of London.

John is widely regarded as the real military leader of the Fitzgeralds.

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.