The days of Queen Elizabeth were now literally numbered. The death of Essex, the intrigues of the King of Scotland, and the successes of Tyrone, preyed upon her spirits. The Irish chief was seldom out of her mind, and, as she often predicted, she was not to live to receive his submission. She was accustomed to send for her godson, Harrington, who had served in Ireland, to ask him questions concerning Tyrone; the French ambassador considered Tyrone's war one of the causes that totally destroyed her peace of mind in her latter days. She received the news of the victory of Kinsale with pleasure, but, even then, she was not destined to receive the submission of Tyrone.

The events of the year, so inauspiciously begun for the Irish arms, continued of the same disastrous character. Castlehaven was surrendered by its Spanish guard, according to Del Aguila's agreement. Baltimore, after a momentary resistance, was also given up, but O'Sullivan, who considered the Spanish capitulation nothing short of treason, threw a body of native troops, probably drawn from Tyrrell's men, into Dunboy, under Captain Richard Mageoghegan, and Taylor, an Englishman, connected by marriage with Tyrrell. Another party of the same troops took possession of Clear Island, but were obliged to abandon it as untenable. The entire strength of the Dunboy garrison amounted to 143 men; towards the end of April - the last of the Spaniards having sailed in March - Carew left Cork at the head of 3,000 men to besiege Dunboy. Sir Charles Wilmot moved on the same point from Kerry, with a force of 1,000 men, to join Carew. In the pass near Mangerton Wilmot was encountered by Donald O'Sullivan and Tyrrell, at the head of then remaining followers, but forced a passage and united with his superior on the shores of Berehaven. On the 1st of June the English landed on Bear Island, and on the 6th opened their cannonade. They were 4,000 men, with every military equipment necessary, against 143. After eleven days' bombardment the place was shattered to pieces; the garrison offered to surrender, if allowed to retain their arms, but their messenger was hanged, and an instant assault ordered. Over fifty of this band of Christian Spartans had fallen in the defence, thirty attempted to escape in boats, or by swimming, but were killed to a man while in the water. The remainder retreated with Mageoghegan, who was severely wounded, to a cellar approached by a narrow stair, where the command was assumed by Taylor. All day the assault had been carried on till night closed upon the scene of carnage. Placing a strong guard on the approach to the crypt, Carew returned to the charge with the returning light. Cannon were first discharged into the narrow chamber which held the last defenders of Dunboy, and then a body of the assailants rushing in, despatched the wounded Mageoghegan with their swords, having found him, candle in hand, dragging himself towards the gunpowder. Taylor and fifty-seven others were led out to execution; of all the heroic band, not a soul escaped alive.

The remaining fragments of Dunboy were blown into the air by Carew on the 22nd of June. Dursey Castle, another island fortress of O'Sullivan's, had fallen even earlier; so that no roof remained to the lord of Berehaven. Still he held his men well together in the glens of Kerry, during the months of Summer, but the ill-news from Spain in September threw a gloom over those mountains deeper than was ever cast by equinoctial storm. Tyrrell was obliged to separate from him in the Autumn, probably from the difficulty of providing for so many mouths, and O'Sullivan himself prepared to bid a sad farewell to the land of his inheritance. On the last day of December he left Glengariffe, with 400 fighting men, and 600 women, children, and servants, to seek a refuge in the distant north. After a retreat almost unparalleled, the survivors of this exodus succeeded in reaching the friendly roof of O'Ruarc, at Dromahaire, not far from Sligo. Their entire march, from the extreme south to the almost extreme north-west of the island, a distance, as they travelled it, of not less than 200 miles, was one scene of warfare and suffering. They were compelled to kill their horses, on reaching the Shannon, in order to make boats of the hides, to ferry them to the western bank. At Aughrim they were attacked by a superior force under Lord Clanrickarde's brother, and Captain Henry Malby, but they fought with the courage of despair, routed the enemy, slaving Malby, and other officers. Of the ten hundred who left the shores of Glengariffe, but 35 souls reached the Leitrim chieftain's mansion. Among these were the chief himself, with Dermid, father of the historian, who at the date of this march had reached the age of seventy. The conquest of Munster, at least, was now complete. In the ensuing January, Owen McEgan, Bishop of Ross, was slain in the midst of a guerilla party, in the mountains of Carberry, and Ms chaplain, being taken, was hanged with the other prisoners. The policy of extermination recommended by Carew was zealously carried out by strong detachments under Wilmot, Harvey, and Flower; Mr. Boyle and the other "Undertakers" zealously assisting as volunteers.

Mountjoy, after transacting some civil business at Dublin, proceeded in person to the north, while Dowcra, marching out of Derry, pressed O'Neil from the north and north-east. In June, Mountjoy was at Charlemont, which he placed under the custody of Captain Toby Caufield, the founder of an illustrious title taken from that fort. He advanced on Dungannon, but discovered it from the distance, as Norris had once before done, in flames, kindled by the hand of its straitened proprietor. On Lough Neagh he erected a new fort called Mountjoy, so that his communications on the south now stretched from that great lake round to Omagh, while those of Dowcra, at Augher, Donegal, and Lifford, nearly completed the circle. Almost the only outlet from this chain of posts was into the mountains of O'Cane's country, the north-east angle of the present county of Derry. The extensive tract so enclosed and guarded had still some natural advantages for carrying on a defensive war. The primitive woods were standing in masses at no great distance from each other; the nearly parallel vales of Faughan, Moyala, and the river Roe, with the intermediate leagues of moor and mountain, were favourable to the movements of native forces familiar with every ford and footpath. There was also, while this central tract was held, a possibility of communication with other unbroken tribes, such as those of Clandeboy and the Antrim glens on the east, and Breffni O'Ruarc on the west. Never did the genius of Hugh O'Neil shine out brighter than in these last defensive operations. In July, Mountjoy writes apologetically to the Council, that "notwithstanding her Majesty's great forces, O'Neil doth still live." He bitterly complains of his consummate caution, his "pestilent judgment to spread and to nourish his own infection," and of the reverence entertained for his person by the native population. Early in August, Mountjoy had arranged what he hoped might prove the finishing stroke in the struggle. Dowcra from Derry, Chichester from Carrickfergus, Danvers from Armagh, and all who could be spared from Mountjoy, Charlemont, and Mount Norris, were gathered under his command, to the number of 8,000 men, for a foray into the interior of Tyrone. Inisloghlin, on the borders of Down and Antrim, which contained a great quantity of valuables, belonging to O'Neil, was captured. Magherlowney and Tulloghoge were next taken. At the latter place stood the ancient stone chair on which the O'Neils were inaugurated time out of mind; it was now broken into atoms by Mountjoy's orders. But the most effective warfare was made on the growing crops. The 8,000 men spread themselves over the fertile fields along the valleys of the Bann and the Roe, destroying the standing grain with fire, where it would burn, or with the praca, a peculiar kind of harrow, tearing it up by the roots. The horsemen trampled crops into the earth which had generously nourished them; the infantry shore them down with their sabres, and the sword, though in a very different sense from that of Holy Scripture, was, indeed, converted into a sickle. The harvest month never shone upon such fields in any Christian land. In September, Mountjoy reported to Cecil, "that between Tulloghoge and Toome there lay unburied a thousand dead," and that since his arrival on the Blackwater - a period of a couple of months - "there were about 3,000 starved in Tyrone." In O'Cane's country, the misery of his clansmen drove the chief to surrender to Dowcra, and the news of Hugh Roe's death having reached Donegal, his brother repaired to Athlone, and made his submission to Mountjoy, early in December. O'Neil, unable to maintain himself on the river, Roe, retired with 600 foot and 60 horse, to Glencancean, near Lough Neagh, the most secure of his fastnesses. His brother Cormac McMahon, and Art O'Neil, of Clandeboy, shared with him the wintry hardships of that last asylum, while Tyrone, Clandeboy, and Monaghan, were given up to horrors, surpassing any that had been known or dreamt of in former wars. Moryson, secretary to Mountjoy, in his account of this campaign, observes, "that no spectacle was more frequent in the ditches of towns, and especially in wasted countries, than to see multitudes of these poor people dead, with their mouths all coloured green, by eating nettles, docks, and all things they could rend above ground."

The new year, opening without hope, it began to be rumoured that O'Neil was disposed to surrender on honourable terms. Mountjoy and the English Council long urged the aged Queen to grant such terms, but without effect. Her pride as a sovereign had been too deeply wounded by the revolted Earl to allow her easily to forgive or forget his offences. Her advisers urged that Spain had followed her own course towards the Netherlands, in Ireland; that the war consumed three-fourths of her annual revenue, and had obliged her to keep up an Irish army of 20,000 men for several years past. At length she yielded her reluctant consent, and Mountjoy was authorized to treat with the arch-rebel upon honourable terms. The agents employed by the Lord Deputy in this negotiation were Sir William Godolphin and Sir Garrett Moore, of Mellifont, ancestor of the Marquis of Drogheda - the latter, a warm personal friend, though no partizan of O'Neil's. They found him in his retreat near Lough Neagh early in March, and obtained his promise to give the Deputy an early meeting at Mellifont. Elizabeth's serious illness, concealed from O'Neil, though well known to Mountjoy, hastened the negotiations. On the 27th of March he had intelligence of her decease at London on the 24th, but carefully concealed it till the 5th of April following. On the 31st of March, he received Tyrone's submission at Moore's residence, the ancient Cistercian Abbey, and not until a week later did O'Neil learn that he had made his peace with a dead sovereign.

The honourable terms on which this memorable religious war was concluded were these: O'Neil abjured all foreign allegiance, especially that of the King of Spain; renounced the title of O'Neil; agreed to give up his correspondence with the Spaniards, and to recall his son, Henry, who was a page at the Spanish Court, and to live in peace with the sons of John the Proud. Mountjoy granted him an amnesty for himself and his allies; agreed that he should be restored to his estates as he had held them before the war, and that the Catholics should have the free exercise of their religion. That the restoration of his ordinary chieftain rights, which did not conflict with the royal prerogative, was also included, we have the best possible evidence: Sir Henry Dowcra having complained to Lord Mountjoy that O'Neil quartered men on O'Cane, who had surrendered to himself, Mountjoy made answer - "My Lord of Tyrone is taken in with promise to be restored, as well to all his lands as to his honour and dignity, and O'Cane's country is his, and must be obedient to his commands." That the article concerning religion was understood by the Catholics to concede full freedom of worship, is evident from subsequent events. In Dublin, sixteen of the principal citizens suffered fine and imprisonment for refusing to comply with the act of uniformity; in Kilkenny the Catholics took possession of the Black Abbey, which had been converted into a lay fee; in Waterford they did the same by St. Patrick's Church, where a Dominican preacher was reported to have said, among other imprudent things, that "Jesabel was dead" - alluding to the late Queen. In Cork, Limerick, and Cashel, the cross was carried publicly in procession, the old Churches restored to their ancient rites, and enthusiastic proclamation made of the public restoration of religion. These events having obliged the Lord Deputy to make a progress through the towns and cities, he was met at Waterford by a vast procession, headed by religious in the habits of their order, who boldly declared to him "that the citizens of Waterford could not, in conscience, obey any prince that persecuted the Catholic religion." When such was the spirit of the town populations, we are not surprised to learn that, in the rural districts, almost exclusively Catholic, the people entered upon the use of many of their old Churches, and repaired several Abbeys - among the number, Buttevant, Kilcrea, and Timoleague in Cork; Quin Abbey in Clare; Kilconnell in Galway; Rosnariell in Mayo, and Multifarnham in West-Meath. So confident were they that the days of persecution were past, that King James prefaces his proclamation of July, 1605, with the statement - "Whereas we have been informed that our subjects in the kingdom of Ireland, since the death of our beloved sister, have been deceived by a false rumour, to wit, that we would allow them liberty of conscience," and so forth. How cruelly they were then undeceived belongs to the history of the next reign; here we need only remark that the Articles of Limerick were not more shamefully violated by the statute 6th and 7th, William III., than the Articles of Mellifont were violated by this Proclamation of the third year of James I.