Although not strictly part of the Nine Years Wars, the Flight of the Earls forms a neat end point for the conflict and sets up a new period in Irish History. The Earls had been fairy treated in many ways by the new King, and yet they fled. The best way to consider this action is in light not of official policy but rather in the rapacious nature of the royal officials carrying out the policy and the fact that had they been accused of a treason, their credit was not in any shape to defend themselves from even baseless accusations:

It is in the doings of Sir John Davies, Attorney-General for Ireland, and of Sir Arthur Chichester, the new Deputy, during their visitation of Ulster in the autumn of 1606, that we may find the real causes of the last scene in the drama of Tyrone's life in Ireland, which led him to take the resolution of departing from the country. His life had been rendered well-nigh intolerable by the constant espionage kept upon his every word and movement, and the sense that his nearest kin were being constantly tempted to report his actions. Long ago he had said that so many eyes were watching him that he could not drink a full bumper of sack but the State was advertised thereof within a few hours after. These men were greedy for the forfeit of his lands, out of which they hoped to reap a share. Added to this was the proclamation of the new king against the Catholics, far more severe and less easy to evade than any that had preceded it. Hugh saw that it was the determination of James and of his agents to Anglicize the North, and to pass the lands to new planters, in spite of all promises and pledges to the contrary.

For Tyrone and the old chiefs there was no more a place in Ireland, and means were certain to be found to oblige the surrender of their ancestral lands to strangers. He saw this being taken in hand all over Ulster, and even if hints that he was personally unsafe were erroneous this was sufficient to decide him to take flight to countries where he was sure that a welcome would await him. Quietly he made his plans, and, though a large party sailed with him, the Government was quite in the dark as to his determination.[4] His final movements were hastened by the arrival of one John Bath, a Drogheda merchant and ship's captain, who had been sent by Cuconnacht Maguire, now in the Low Countries or Brittany, to tell him that they had brought a ship round to Rathmelton, on Lough Swilly, and were taking in food and drink preparatory to their return; Bath urged the importance of not losing this opportunity of leaving the country.

Tyrone was at Slane with Chichester, trying to settle the bounds of the lands about Dungannon and Charlemont which he had consented to surrender. He had just heard rumours that Chichester was to be appointed President of Ulster, and it did not seem likely that the relations between him and the new President would be cordial. The rumour was unfounded, for Sir Arthur retained the post of Deputy, but it may have influenced O'Neill's decision. He determined to go, and sent Bath on to Ballyshannon to acquaint Rory O'Donnell with his resolution. On September 8, 1607, he took leave of the Deputy, who returned to Dublin, and then went to spend his two last nights in Ireland at Mellifont at the house of his friend Sir Garrett Moore, the fosterer of his son John. It was observed that on his departure he wept abundantly, taking farewell of every child and servant in the house in turn. In the hurry of the flight one of Tyrone's children and one of Caffar O'Donnell's babes were left behind, being away in the charge of their foster-parents; but a company of ninety-nine persons embarked, of whom the more important were—besides O'Neill and his countess, and three of their children—Rory O'Donnell, Earl of Tyrconnel, his brother Caffar, and his sister Nuala, with the attendants belonging to each. Among Tyrone's household was his English secretary, Henry Ovington, in whom he put such confidence that he had been included in all Tyrone's conferences with Essex. He seems to have had no warning of what was on foot, and he later prayed the Government for permission to return. Among the others went Tadhg O'Keenan, from whose interesting account of the adventures of which he was an eyewitness we learn the future events in the lives of the distinguished party.

After a stormy voyage which drove them up the Channel, and made a landing on the coast of Spain impossible, they reached the little town of Quilleboeuf, at the mouth of the Seine, and proceeded by boats up the river to Rouen, whence by a leisurely route they found their way into Flanders, being everywhere treated with the greatest kindness and every mark of respect. Before arriving at Brussels they were met by O'Neill's eldest son, Colonel Henry O'Neill, at the head of his troop of Irish soldiers in the service of Spain, and on the following Saturday the Spanish commander-in-chief in Flanders, the Marquis Spinola, one of the most brilliant soldiers of his age, came to welcome them with a splendid retinue of nobles, and invited them to a banquet on the following day. They were equally courteously received and entertained by the Archduke and Archduchess, the latter being the daughter of the King of Spain, and they met many notables, including the Duc d'Aumale, Cardinal Bentivoglio, the author of the History of the Wars in Flanders, and others. They spent the winter in the Low countries, visiting Douai, Mechlin, Louvain, Antwerp, and other cities, and in the spring continued their journey into Italy. From Louvain the two Earls had drawn up and forwarded to King James a full and dignified statement of the grievances for which they were obliged to leave their native land; these fully explain the causes of their flight.

They left behind them in Brussels the young boys John and Brian, who became pages to the Archduke, and the other children, one of whom was in the future to become the famous Owen Roe O'Neill, Tyrone's half-nephew. Nuala, who had been Niall Garbh's wife, but had been forced to leave him, also remained behind. The rest of the party arrived in Rome in the beginning of May 1608. But the summer heat and malarial fever laid their hand upon Tyrconnel. He and his brother Caffar sank within a few weeks of each other, and were buried in a tomb which is still a resort of Irish visitors in the Church of S. Pietro Montario, on the Janiculum. The thoughts of their sister Nuala on hearing of their death are given voice to in Mangan's well-known verses, "O woman of the piercing wail," founded upon a fine poem by Owen Roe-Mac an Bhaird (or Ward), the family bard.[6] Hugh O'Neill lived on for many years, but he had sorrow upon sorrow. His anxiety for his scattered family must have been great. His son Hugh, Baron of Dungannon, was stricken down soon after the O'Donnells and followed them to the tomb. Tyrone happily did not live to hear the fate of his young son Brian, who was mysteriously and foully murdered in Brussels in 1617; but the babe left behind in his flight had fallen into Chichester's hands, and anxiety for its safety must often have weighed heavily upon him.

Hugh passed away in 1616, aged, blind, and bowed with griefs. There were qualities of real greatness in O'Neill; wise, patient, and acute, in the difficult days in which he lived he played his part with skill and dignity, worthy of dealings with better men. We feel that he had a right to ask that the term 'rebel' should not be applied to him more often than was convenient, and that his persecutors should remember that he was a nobleman born.

TEXT FROM A History of Ireland by Eleanor Hull