Unwilling or unable to pronounce the correct name of the area - 'Deasmumhain', or 'South Munster' - they coined instead the English title Desmond. Previous English conquerors had taken the area and now ruled in what were in effect almost independent principalities. Their leaders were nominally under the Queen.

The provinces of Munster and southern Leinster were dominated, as they had been for over two centuries by the Old English Butlers of Ormonde and Fitzgeralds of Desmond. Both houses raised their own armed forces and imposed their own law, a mixture of Irish and English customs independent of the English government of Ireland in Dublin. They had maintained the old religion too, another bugbear with the English authorities in Dublin and in London. 

Had these houses and their leaders – with other Old English and Irish - acted in concert, they might well have survived the onslaught to come but, if anything, they were more antagonistic to one another than to the English authorities who wished to suppress them. As often, the English exploited this internecine antipathy. 

As we have learned already in relation to Bagenal in the North, the English planned to replace local leaders with provincial presidents (military governors, in effect) and it was in pursuit of this planned policy that Lord Deputy Sidney undertook to confront the Geraldines (the Fitzgerald leaders of Munster) and the Ormondes (Butlers). 

The ‘rebellions’ were primarily about the independence of lords from their monarch but as they progressed they had an increasingly important element of religious conflict. This contributed to the heightened brutality of the subsequent repression. The result of the rebellions was the destruction of the Desmond dynasty and the subsequent plantation of Munster with English settlers.

The local dynasties saw the presidencies as intrusions into their sphere of influence and into their traditional violent competition with each other. This had seen the Butlers and Fitzgeralds fight a pitched battle against each other at Affane in Waterford in 1565. 

Queen Elizabeth summoned the heads of both houses to London to explain their actions.  However, the treatment of the dynasties was not even handed.   Thomas Butler (Earl of Ormonde) who was the Queen's cousin was pardoned, while (in 1567)  both Gerald Fitzgerald,  Earl of Desmond and his brother, John of Desmond, widely regarded as the real military leader of the Fitzgeralds, were arrested and detained in 1568 in the Tower of London - on Ormonde’s urging.

This removed the natural leadership of the Munster Geraldines and left the Desmond Earldom in the hands of a soldier, James Maurice Fitzgerald, the "captain general" of the Desmond military.   Fitzmaurice perceived no role for himself in the proposed new order in Munster, which envisaged the abolition of the Irish lords’ private armies.  

A factor that drew wider support for Fitzmaurice was the prospect of land confiscations, which had been mooted by Sidney and Peter Carew, an English colonist.  This ensured Fitzmaurice the support of important clans, notably MacCarthy Mor, O'Sullivan Beare and O'Keefe and, indeed two prominent Butlers –brothers of the Earl.  

Fitzmaurice himself had lost the land he had held at Kerricurrihy in Cork which had been leased instead to English colonists.   He was also a devout Catholic, influenced by the Counter-Reformation which 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 planned a military strike against the English presence in the south and against the Earl of Ormonde.  

Fitzmaurice however had wider aims than simply the recovery of Fitzgerald supremacy. Before the rebellion, he secretly sent Maurice MacGibbon Catholic Archbishop of Cashel  to seek military aid from King Philip II of Spain.

Fitzmaurice launched his insurrection in June 1569 by attacking the English colony at Kerrycurihy before attacking Cork itself and those native lords who refused to join the rebellion.   Fitzmaurice’s force of up to 4,500 men went on to besiege Kilkenny, seat of the Earls of Ormonde in July.   

In response, Sidney mobilised 600 English troops, who marched south from Dublin and another 400 troops landed by sea in Cork.  Thomas Butler, Earl of Ormonde returned from London where he had been at court, brought the rebel Butlers out of the rebellion and mobilised Gaelic Irish clans antagonistic to the Geraldines. 

Together, Ormonde, Sidney and Humphery Gilbert, appointed as governor of Munster, began devastating the lands of Fitzmaurice's allies.  As Bagenal was Marshall and fought in this campaign, we must assume at the very least that he was a willing participant in all that followed.

As individual lords felt compelled to retire to defend their own territories under this onslaught, Fitzmaurice's forces broke up.  Gilbert in particular was notorious for the terror tactics he employed, killing civilians at random and setting up a corridor of severed heads at the entrance to his camps.

In late 1569 a similar but shorter insurrection broke out in England, but was quickly crushed.  This and the Desmond Rebellion caused the Pope in early 1570 to issue in support "Regnans in Excelcis”.  This became the excuse needed by the English authorities for their ever more barbarous actions and Queen Elizabeth's previous acceptance of Roman Catholic worship in private turned into a more active suppression of organised Catholic services.

Sidney forced Fitzmaurice into the Kerry Mountains, from where he launched hit and run attacks on the English and their allies.  By 1570 most of Fitzmaurice's allies had submitted to Sidney.  The most important, Donal MacCarthy Mor surrendered in November 1569.  Nevertheless, the guerrilla campaign dragged on for three more years.

In February 1571, John Perrot was made Lord President of Munster, pursuing Fitzmaurice with 700 troops for over a year without success.  Fitzmaurice had some victories, capturing an English ship near Kinsale and burning the town of Kilmallock in 1571, for example, but by early 1573, his force was reduced to less than 100 men.

Fitzmaurice finally submitted on February 23, 1573, having negotiated a pardon for his life.  However in 1574, he again became landless and in 1575 he sailed to France to seek help from the Catholic powers to start another rebellion.

Gerald Fitzgerald, Earl of Desmond, and his brother John were released from prison to stabilise the situation and to reconstruct their shattered territory.  Under a new settlement imposed after the rebellion, known as "composition", the Desmond’s military forces were limited by law to just 20 horsemen and their tenants made to pay rent to them rather supply military service or to quarter their soldiers.  

Perhaps the biggest winner of the first Desmond Rebellion was the Earl of Ormonde, who established himself as loyal to the English Crown and as the most powerful lord in the south of Ireland.

Although all of the local chiefs had submitted by the end of the rebellion, the methods used to suppress it provoked long-lasting resentment, especially among the Irish mercenaries, gall oglaigh or "gallowglass" as the English termed them, who had rallied to Fitzmaurice.   

William Drury, the new Lord President of Munster from 1576, executed around 700 of them in the years after the rebellion.  Furthermore, in the aftermath of the rebellion, Gaelic customs such as Brehon Laws, Irish dress, bardic poetry and the maintaining of private armies were again outlawed – things that were highly provocative to traditional Irish society but which would have met with Bagenal’s approval.

Fitzmaurice had deliberately emphasized the Gaelic character of the rebellion, wearing the Irish dress, speaking only Irish and referring to himself as the captain (taoiseach) of the Geraldines.  

Finally, Irish landowners continued to be threatened by the arrival of English colonists.  All of these factors meant that, when Fitzmaurice returned from continental Europe to start a new rebellion, there were plenty of discontented people in Munster waiting to join him.

The second Desmond rebellion was sparked when James Fitzmaurice Fitzgerald launched an invasion of Munster in 1579.  During his exile in Europe, he had reinvented himself as a soldier of the counter-reformation, arguing that since the Pope’s excommunication of Elizabeth I in 1570 Irish Catholics no longer owed loyalty to a heretic monarch. The Pope granted Fitzmaurice an "indulgence" and supplied him with troops and money.

Fitzmaurice landed at Smerwick, near Dingle on July 18, 1579 with a small force of Spanish and Italian troops.  He was joined in rebellion on August 1 by John of Desmond, a brother of the Earl, who had a large following among his kinsmen and the disaffected swordsmen of Munster. Other Gaelic clans and Old English families also joined in the rebellion.  After Fitzmaurice was killed in a skirmish with the Clanwilliam Burkes on August 18, John Fitzgerald assumed leadership of the rebellion.

Gerald, the Earl of Desmond, initially resisted the call of the rebels and tried to remain neutral but joined in once the authorities proclaimed him a traitor.  The Earl joined the rebellion by sacking the towns of Youghal (on November 13) and Kinsale, and devastated the country of the English and their allies.

However by the summer of 1580 English troops under William Pelham and locally raised Irish forces under the Earl of Ormonde succeeded in bringing the rebellion under control, re-taking the south coast, destroying the lands of the Desmonds and their allies in the process, and killing their tenants.  By capturing Carrigafoyle at Easter 1580, the principal Desmond castle at the mouth of Shannon river, they cut off the Geraldine forces from the rest of the country and prevented a landing of foreign troops into the main Munster ports. It looked as if the rebellion was fizzling out.

However, in July 1580, the rebellion spread to Leinster, under the leadership of Gaelic Irish chieftain Fiach MacHugh O'Byrne and the Pale Lord Viscount Baltinglass—motivated by Catholicism and hostility to the English.  A large English force under the Lord Deputy of Ireland Earl Grey de Wilton were sent to subdue them, only to be ambushed and massacred at the battle of Glenmalure on August 25, losing over 800 dead. However, the Leinster rebels were unable to capitalise on their victory or to effectively coordinate their strategy with the Munster insurgents.

On September 10, 1580, 600 Papal troops landed at Smerwick in Kerry to support the rebellion, but were besieged in a fort at Dun an Oir. They surrendered after two days of bombardment and were then massacred.  By relentless scorched-earth tactics, the English broke the momentum of the rebellion by mid 1581.  By May 1581, most of the minor rebels and Fitzgerald allies in Munster and Leinster had accepted Elizabeth I's offer of a general pardon.  Even worse, John of Desmond, in many ways the main leader of the rebellion, was killed north of Cork in early 1582.

For the Geraldine Earl however there would be no pardon, and he was pursued by crown forces until the end.  From 1581 to 1583, the war dragged on, with the remaining Geraldines evading capture in the mountains of Kerry. The rebellion was finally ended on 2 November 1583 when the earl was hunted down and killed near Tralee in Kerry by the local clan O'Moriarty.  The clan chief, Maurice, received 1000 pounds of silver from the English government for Desmond's head, which was sent to Queen Elizabeth.  His body was triumphantly displayed on the walls of Cork.

After three years of English scorched earth warfare, famine devastated Munster.  In April 1582, the provost marshal of Munster, Sir Warham St Leger estimated that 30,000 people had died of famine in the previous six months.  Plague broke out in Cork city where the country people fled to avoid the fighting.  People continued to die of famine and plague long after the war had ended, and it is estimated that by 1589 one third of the province's population had died.

Following a survey begun in 1584 by Sir Valentine Browne, Surveyor General of Ireland, the thousands of English soldiers and administrators who had been imported to deal with the rebellion were allocated land in the Munster Plantation of Desmond's confiscated estates.

The Elizabethan conquest of Ireland was completed after the subsequent Nine Years War in Ulster and the extension of plantation policy to other parts of the country.