The Nine Years War (Irish: Cogadh na Naoi mBliana) during the Early Modern Period, in Ireland took place from 1594 to 1603 and is also known as Tyrone's Rebellion, was the last major struggle to preserve Gaelic Ireland. It was fought between the forces of Gaelic Irish chieftains Hugh Ó Neill (Earl of Tyrone), Hugh Roe O'Donnell and their allies, against the Elizabethan English government of Ireland. It ended in defeat for the Irish chieftains, which led ultimately to their exile in the Flight of the Earls and to the Plantation of Ulster. The MacMahons continued to fight among themselves while Hugh Ó Neill had not yet officially joined the war and continued to build alliances in preparation. The Nine Years War was caused by the collision between the ambition of the Gaelic Irish chieftain Hugh Ó Neill and the advance of the English state in Ireland, from control over the Pale to ruling the whole island. Hugh Ó Neill came from the powerful Ó Neill sept (or clan) of Tyrone, who dominated that centre of the northern province of Ulster. His father was killed and he was banished from Ulster as a child by Shane Ó Neill. From Red Hugh O'Donnell, his ally, he took a supply of Scottish mercenaries (known as Redshanks; he also hired large contingents of Irish mercenaries known as buanadha under leaders such as Richard Tyrell.

In 1591, William Fitzwilliam broke up the MacMahon lordship in Monaghan when The MacMahon, hereditary leader of the sept, resisted the imposition of an English sheriff; he was hanged and his lordship divided. There was an outcry, with several sources alleging corruption against Fitzwilliam, but the same policy was soon applied in Longford (territory of the O’Farrells) and Breifne (Cavan — territory of the O’Reillys). Any attempt to further the same in the Ó Neill and O’Donnell territories was bound to be resisted by force of arms. Tragically, during the Battle of Kinsale on December 24, 1601 O'Donnell launched an attack to break the English siege but was defeated by Sir Charles Blount, Lord Mountjoy. Ireland had been a lordship under the authority of the English Crown since the twelfth century; but by the 1500s, the area under government control had shrunk to the Pale , the area around Dublin. The first major conflict this caused was the Desmond Rebellions between 1569 and 1583.

Following the destruction of the Spanish Armada in 1588 and the failure of subsequent naval expeditions to northern Europe, Phillip III remained hopeful of defeating English influence. Phillip sent Don Juan de Aguila and Don Diego Brochero to Ireland with 6,000 men, and a significant amount of arms and ammunition. Accompanying them was the controversial Jesuit, James Archer. One of the ships, carrying the majority of veteran soldiers and gunpowder, failed to make it to Ireland. The remaining 3,400 men disembarked at Kinsale, just south of Cork on October 2, 1601, at the opposite end of the island from the rebel stronghold of Ulster. Lord Mountjoy's forces were incapable of surrounding the town of Kinsale, but they did seize some higher ground and subjected the Spanish forces to regular artillery fire. The English cavalry rode through the surrounding countryside destroying livestock and crops, while both sides called for allegiance from the population. Ó Neill and O'Donnell were hesitant about leaving Ulster open to attack by marching south. Meanwhile, a small group of reinforcements arrived from Spain to aid the Irish. The Irish and Spanish together organized the main engagement, on December 24, 1601 (British date: January 3, 1602 for the Catholic army). They formed into three columns, led by Richard Tyrell, Hugh Ó Neill, and O'Donnell. They marched toward a night attack, but owing to a lack of coordination and possible arguments between the commanders, they failed to reach their destination by dawn. Mountjoy led his forces to meet the enemy at a ridge northwest of the city. Aguila mistook the sounds of battle for an English ruse to draw him out, and only took action when he mistook the approaching English forces for returning Irish. The English resumed their attacks upon the little town of Kinsale, eventually breaching the defences, taking the town, and agreeing to a peace settlement with Aguila. This loss put an end to Spanish ambitions in Ireland and to much of the Irish resistance. Spain and England agreed a temporary peace with the signing of the Treaty of London. The Ulster lords were granted terms of surrender that many considered generous. This resulted in the Flight of the Earls, when the principal Gaelic leaders of Ulster, including Ó Neill himself, boarded ship and set themselves up in exile in France, Spain and Italy. Their intention was always to raise an army and oust English authority in their home province, but the territories they had left behind were soon divided up in the Plantation of Ulster, and they were never allowed to return.

In September 1607 a French ship sailed from the northern harbour of Rathmullan in Lough Swilly. On board were Hugh Ó Neill, Earl of Tyrone, and Rory O'Donnell, Earl of Tyrconnell, together with more than ninety of their family and followers. The ship was bound for Spain, but fierce storms forced them to disembark in France in early October. Thereafter they made their way to Rome, where they remained in voluntary exile, and where Ó Neill died in 1616. As a boy, Hugh Ó Neill had been taken into the care of Elizabeth's viceroy, Sir Henry Sidney, and raised as an English nobleman. After returning to his native County Tyrone, he had shown his loyalty by helping to suppress the Desmond rebellion in Munster. In 1587 he was recognised as Earl of Tyrone, and was granted extensive territory under the Crown. A year later, however, he ignored a government order to execute survivors of the Spanish armada who landed in Ireland, and in Dublin there were increasing doubts about Ó Neill's loyalty. Ó Neill was allowed to keep 600 men in arms at the Queen's expense, and by regularly changing them he was able to train a substantial army. Lead to roof his new castle at Dungannon was turned into bullets. In Connacht, the Gaelic lords had submitted to the Crown. In Munster, following the defeat of the second Desmond rebellion in 1583, English settlers had acquired confiscated land. In Ulster, though, there were no English settlers or garrisons west of Lough Neagh. With its mountains, lakes and forests, the region was eminently defensible, and Ó Neill found a vigorous ally in Red Hugh O'Donnell of Tyrconnell, who had escaped from imprisonment in Dublin. In 1593, Ó Neill took the now illegal Gaelic title of "The Ó Neill" and prepared to lead the Ulster chiefs in defence of territory and religion. Ó Neill was a skilful commander, and his troops exploited the difficult terrain to harry the English columns.

As the Irish responded in 1593, Hugh Ó Neill, Earl of Tyrone, took the 'illegal' Gaelic title of "The Ó Neill" and prepared to lead the Ulster chiefs in defence of territory and religion. Seeing their days numbered by forces destined to completely erode their power, the Irish continued the struggle in 1594, spearheaded by Red Hugh O'Donnell of Tyrconnell, who defeated an English army at the 'Ford of the Biscuits'. Hugh Ó Neill was educated for eight years in England, and became Earl of Tyrone in 1585. For some years it seemed that he would remain loyal to the Crown, but in 1595, seven years after the Spanish Armada, Ó Neill and Hugh O'Donnell rose in rebellion and appealed for Spanish help. The Irish in Ulster, led by Hugh Ó Neill, Ulster's "principle chieftain," succeeded among other places, at the Battle of Yellow Ford, County Armagh, in 1598 convincing Elizabeth I that more resources would have to be committed to her army in Ireland.

In 1595, Ó Neill officially endorsed the inauguration of Brian Mac Hugh Og as 'MacMahon' and supported an invasion of Farney that restored Ever Mac Con Uladh to his ancestral home. By these acts, Ó Neill gained the support of two of the important MacMahon leaders. Shortly afterward, Hugh Ó Neill joined the war against the English. In 1595, Ó Neill won a handsome victory at Clontibret, near Monaghan, over an army commanded by his brother-in-law, Sir Henry Bagenal. Bagenal was to lose his life during the Battle of the Yellow Ford, on the River Blackwater, in 1598. This was Ó Neill's greatest triumph. In 1601 he made the mistake of marching to the southern port of Kinsale to join an invading Spanish army, and the Irish were routed in unfamiliar country. O'Donnell fled to Spain, but Ó Neill returned to Tyrone. At the battle of the Yellow Ford in 1598 up to 2000 English troops were killed in battle having been ambushed on the march to Armagh. Ó Neill's personal enemy, Henry Bagenal, had been in command of the army and was killed during the early engagements. It was the heaviest defeat ever suffered by the English army in Ireland up to that point. Hugh Ó Neill appointed his supporters as chieftains and earls around the country, notably James Fitzthomas Fitzgerald as the Earl of Desmond and Florence MacCarthy as the MacCarthy Mór. In Munster as many as 9000 men came out in rebellion. The Munster Plantation, the colonisation of the province with English settlers, was utterly destroyed, the colonists, among them Edmund Spenser, fled for their lives. Only a handful of native lords remained consistently loyal to the crown and even these found their kinsmen and followers defecting to the rebels. However all the fortified cities and towns of the country sided with the English colonial government

By 1597 things looked well for Ó Neill. But the arguing among the MacMahons continued and Ó Neill was not able to keep them together as allies. In 1598, the yeare of Ó Neill's greatest victories, Patrick Mac Art Moyle claimed title of MacMahon in opposition to Brian Mac Hugh Og. In 1600 Baron Mountjoy led the English efforts against Ó Neill. His strategy was to surround Ó Neill on all sides and by May 1601 Mountjoy could claim that Farney, the Fews in Armagh, Clancarrol, the O'Hanlons, as well as many of the MacMahons and O'Reillys were 'reduced'. The MacMahons who surrendered to Mountjoy included Ever Mac Con Uladh, Patrick Mac Art Moyle, Art Mac Rory Mac Brian, and Brian, the brother of Red Hugh. Meanwhile, Brian Mac Hugh Og was still at large and continued to fight. The population of Ireland in 1600 may not have been much more than 1 million. In September 1601 the Irish, including Hugh Ó Neill and Brian Mac Hugh Og suffered a major defeat at Kinsale. Ó Neill and Brian Mac Hugh Og held out for almost two more years, attempting to negotiate a favorable surrender. But Mountjoy had invaded and retaken Monaghan and would not come to terms. In March, 1603 Brian Mac Hugh Og, the last of the MacMahons to do so, surrendered. Later that yeare Ó Neill surrendered, bringing an end to the Nine Years War. England had now completed their conquest of Ulster.

In 1599, Robert Devereux, 2nd Earl of Essex arrived in Ireland with over 17,000 English troops. He took the advice of the Irish privy council, to settle the south of the country with garrisons before making an attempt on Ulster. Those expeditions he did organise were disastrous, especially an expedition crossing the Curlew mountains to Sligo, which was mauled by O’Donnell at the Battle of Curlew Pass. Thousands of his troops, shut up in unsanitary garrisons, died of diseases such as typhoid and dysentery. Two veterans of Irish warfare, George Carew and Arthur Chichester, were given commands in Munster and Ulster respectively. Carew managed more or less to quash the rebellion in Munster by mid 1601, using a mixture of conciliation and force. By the summer of 1601 he had retaken most of the principal castles in Munster and scattered the rebel forces. Fitzthomas and Florence MacCarthy were arrested and kept captive in the Tower of London, where both eventually died. Most of the rest of the local lords submitted once Ó Neills mercenaries had been expelled from the province. In 1601, the long promised Spanish expedition finally arrived in the form of 3500 soldiers at Kinsale, Cork, virtually the southern tip of Ireland. Mountjoy immediately besieged them with 7000 men. Ó Neill, O’Donnell and their allies marched their armies south to sandwich Mountjoy, whose men were starving and wracked by disease, between them and the Spaniards. On the 24 of December, Ó Neill and O’Donnell took the decision to attack the English. The rebels however were not used to fighting pitched battles and were routed by the English forces in what is known as the battle of Kinsale. Mountjoy smashed the Ó Neill’s inauguration stone at Tullaghogue, symbolically destroying the Ó Neill clan. Famine soon hit Ulster as a result of the English scorched earth strategy.

Until 1603 when Hugh Ó Neill, Earl of Tyrone, submitted to the English at Mellifont, all the forested land west of Lough Neagh was Tyrone Country where Ó Neill. To avoid being murdered by his uncle which is what happened to his father - Ó Neill had been sent to Sussex to be educated by Sir Henry Sydney. There are reminders of the green gaiety of the ancient wood around Springhill, a 17th-century fortified house near Moneymore. A thicket of old yews has survived and the lrish oak stairway came from local forests. Moneymore itself is a typical plantation town, with a market house, dispensary,and other fine buildings in the wide main street. Built by the Drapers Company, it was the first town in Ulster to have piped water. In 1603 Ó Neill submitted to the Queen's representative, Lord Mountjoy, as O'Donnell's brother Rory had earlier done. However, despite a generous settlement in which he retained his earldom, Ó Neill found English rule unacceptable. In 1605, the new Lord Deputy of Ireland, Arthur Chichester, began to restrict the freedoms of the two earls. The two decided to flee to the Continent. When the flight of the earls denuded Ulster of its Gaelic aristocracy in 1607, the government took the opportunity to confiscate six of the nine Ulster counties. The subsequent plantation of Ulster, introducing Protestant settlers from England and Scotland, laid the foundation of today's divided island. The Ó Neill dynasty claimed descent from the Ui Neill line which derived its origins from the ancient hero, Niall of the Nine Hostages, and the sons of Banbha. After the Flight of the Earls in 1607, Sir Donnell Ballagh O'Cahan, Chief of the O'Cahan (and at one time knighted by the English Crown), was captured and sent to the Tower of London, where he died in 1626. There has been no Chief since.

Tadhg Ó Cianáin, fl. 1600, was the author of a journal-style chronicle of the Flight of the Earls from Donegal to Rome between September 1607 and April 1608. In 1627. while collecting materials for what would become the Annals of the Four Masters, Mícheál Ó Cléirigh made use of some hagiographical written by him, since lost.

The Contention of the Bards (in Irish, Iomarbhágh na bhFileadh) was a literary controversy of early 17th century Gaelic Ireland, lasting from 1616 to 1624 (probably peaking in 1617), in which the principal bardic poets of the country engaged in a bout of polemical versifying against each other and in support of their respective patrons. There were thirty contributions to the Contention (not published in print until the 19th century), which took the form of a bitter debate over the relative merits of the two halves of Ireland - the north dominated by the Eremonian descendants of the Milesians, and the south dominated by the Eberian descendants. The occasion for the Contention was a dispute over the allegiance of the Earl of Thomond, a Gaelic nobleman of the ancient O'Brien clan (or sept) - unusually for the time, the earl was a Protestant and loyal to the new dispensation. In 1616 the Earl of Thomond's bard, Tadhg Mac Dáire Mac Bruaideadha, wrote verses attacking the semi-legendary bard Torna Éigeas, on account of historical inaccuracies in his work and his partiality to the northern half of Ireland and the Eremonian branches of the Gael. Some of the participants in the Contention mocked the principal debate between Tadhg and Lúghaidh. The spark came in 1616, after the final annexation of the modern County Clare (containing part of the ancient kingdom of Thomond) to the Eberian province of Munster (whereupon the Earl of Thomond was appointed president of the province) and the death in exile of the last great Eremonian, Hugh Ó Neill (Aodh Mór Ó Néill b.1540 – 20 July 1616) 2nd Earl of Tyrone (known as the Great Earl).

When James I succeeded Queen Elizabeth in 1603, he resumed the plantation of English and Scottish settlers with a vengeance, especially in the part of Ireland which had been the center of the uprising: Ulster. Threatened by all the newcomers, Ó Neill and about one hundred of the most important people in Ulster fled the country from Rathmullan, County Donegal in 1607. In 1610, the settlement in County Coleraine (Derry) by a group of London livery companies caused the name of the county to be changed to Londonderry. In 1622 little more than 13,000 Protestants lived in Ulster, yet by 1641 their population was over 100,000. Within 30 years of the arrival of James’ first settlers, only slightly more than 10 per cent of Ulster still belonged to the Catholic native Irish.

The English attorney general, John Davies described the area as 'the wastest and wildest part of all the north'. Davies further described the MacMahons at the 'proudest and most barbarous sect among the Irish'. By 1640 local ownership of lands went from seventy eight to forty six percent. Slowly, the Irish nobles sold off their lands in order to meet their tax obligations and rate payers. Prior to the 1641 Rising, the MacMahons are listed in the tax records as owning some 78 townlands, rivaling Scottish settlers in Fermanagh and British settlers in Louth. After the wars, the MacMahons are no longer listed as landowners in County Monaghan and 112 Mac Mahons listed in the Pender's Census in Monaghan in 1659. The once great Kingdom of Oriel that had lasted for some 1300 years came to an end. During 1641, the Irish revolted again, establishing a national parliament in Kilkenny which stood not only for independence but for full liberty of religion and conscience of nearly eighty percent of the land in Ireland belonged to Catholics. Worse followed when the English Parliament declared that after May 1, 1654, under penalty of death, no Irish could live east of the River Shannon and only those who could prove they had not been rebels could own land west of the Shannon. All the land east of the Shannon was divided among Protestant settlers.