In September 1607 a French ship sailed from the northern harbour of Rathmullan in Lough Swilly. On board were Hugh O'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 O'Neill died in 1616.

For centuries the native Irish had struggled to preserve the Gaelic way of life, with its distinct laws and customs. Through inter-marriage many of the Norman conquerors had become 'more Irish than the Irish', until the King of England's rule had been confined to a small area around Dublin known as the Pale. During the sixteenth century, successive Tudor monarchs tried to extend their authority, but there was always strong resistance from the northern province of Ulster. Religion became a factor in the struggle. Soon after the Protestant Queen Elizabeth came to the English throne in 1558, an Irish parliament passed an Act of Supremacy confirming her as head of the Irish Church, and requiring office-holders in church and state to swear allegiance to her. The Gaels and their "Old English" allies remained staunchly loyal to the Roman Catholic Church.

As a boy, Hugh O'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 O'Neill's loyalty. The doubts were justified. O'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.

Elsewhere in Ireland, English government was tightening its grip. 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 O'Neill found a vigorous ally in Red Hugh O'Donnell of Tyrconnell, who had escaped from imprisonment in Dublin. In 1593, O'Neill took the now illegal Gaelic title of "The O'Neill" and prepared to lead the Ulster chiefs in defence of territory and religion.

O'Neill was a skilful commander, and his troops exploited the difficult terrain to harry the English columns. In 1595, he 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 O'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.