For the first time Englishmen and Irishmen were to be equal in the sight of the law, "every man indiscriminately taken into the favour of the King's majestie." The whole country was divided into shires, and the judges went on circuit as in England, theoretically enforcing the law upon noble and peasant. The English method of holding land and of hereditary succession were made obligatory, a system advantageous to the chiefs, who became sole owners of their land, which had hitherto been held on a loose kind of joint ownership with other members of the clan.

Great hopes had been entertained by the Catholics when James succeeded to the throne, for as the son of so devoted a Catholic as Mary, Queen of Scots, he was thought likely to grant toleration. But James had never shown any sympathy to his mother's faith, and he certainly could not have granted complete religious freedom, even if such a thing were possible under the existing conditions, owing to the strong Protestant feeling of his British subjects. At this time five-sixths of the Irish people were Catholics, whose priests were much under the power and authority of Rome, hating everything English. When it was known that the king was going to continue the Catholic disabilities, there was some trouble in Munster, where a certain Jesuit named White ordered Mass to be said publicly in the churches. A few Anglican clergy were forced to flee, but Mountjoy, the Viceroy, soon crushed the rising without recourse to any barbarities.

The sunshine of prosperity did not long shine upon Tyrone. Little or no evidence exists to prove that he was planning another rising, but apparently, hearing rumours that he was in danger, he fled, together with Tyrconnel and their families. They reached Rome, where they died not long afterwards. Flight was taken as evidence of guilt, the two Earls were declared traitors, and their lands, consisting of the six counties of Ulster—Armagh, Cavan, Londonderry, Fermanagh, Tyrone, and Donegal—declared forfeit to the Crown. Profiting by the mistakes of former plantations, no large tracts of lands were to be distributed to any one owner, for each new landlord was to dwell on his estate, which was to be farmed by men of English or Scottish blood. Bacon, with the assistance of Sir John Davies, Solicitor-General of Ireland, was responsible for this scheme, which turned out successful from the colonizing point of view. Ulster grew prosperous, the new farmers were industrious men getting the best out of the land, and manufactures were introduced. But the native Irish, who had been dispossessed, driven out to the hills and waste parts of the province, became more and more filled with a bitter enmity against their rulers, an enmity which was to find a terrible expression a generation later.

Englishmen were eager to get new land, and if it could be obtained without the trouble of crossing the Atlantic Ocean, and facing the dangers of an unknown continent, so much the better. Ireland became the prey for greedy adventurers, and no man's land was secure. As Judge O'Connor Morris states: "Obsolete claims to lands were set up by descendants of colonists of Plantagenet times; hundreds of ancient royal grants were declared invalid; the right of the Crown to large domains was asserted with success; legal ingenuity and chicane were taxed to pick out flaws in titles." Many of the landowners in Connaught had not obtained title-deeds when their property was changed into a feudal tenure, but they secured possession for a short time (it was only a respite) by the payment of a large sum of money. Men of English blood, hitherto loyal, began to join with the native Irish, fearing the loss of their ancestral property.

To give legal form to the Plantation of Ulster and the attainder of the earls, a Parliament was summoned to Dublin in 1613. In order to obtain a Protestant majority (Catholics being now admitted), forty new boroughs were manufactured in Ulster, consisting of the towns yet to be built, not discoverable on any map, but which were entitled to send two members to Parliament. This naturally provoked the greatest indignation; but though James allowed a petition to be presented to him, little redress was obtained, and through the new borough members the Plantation was duly confirmed.

Towards the end of James 's reign, Ireland, from a superficial point of view, seemed both peaceful and prosperous. The unhappy conditions prevailing in 1603, after the long and disastrous wars of Elizabeth's reign, had improved somewhat, and the new settlers had undoubtedly raised the prosperity of the country. That Ireland itself was a desirable place, in spite of its backwardness, Sir John Davies has left us a record, telling us of "the good temperature of the air; the fruitfulness of the soil; the pleasant and commodious seats for habitation; the safe and large ports and havens lying open for traffic into all the west parts of the world; the long inlets of many navigable rivers, and so many great lakes and fresh ponds within the land, as the like are not to be seen in any part of Europe; the rich fishings and wild-fowl of all kinds; and, lastly, the bodies and minds of the people endued with extraordinary abilities of nature." But underneath this fair semblance the native Irish were brooding over their wrongs in sullen discontent, half starved, robbed of their lands, and deprived of their chiefs.

When Charles succeeded his father he promised certain favours, known as "Graces," to the Connaught landowners, assuring them that sixty years' possession of their land was sufficient title-deed, and in return he obtained £ 120,000 from the grateful owners. These concessions were to be confirmed by Parliament, which was to be called immediately. Doubtless owing to the trouble he was caused by the English Parliament, Charles did not summon a Parliament, and his promises remained unratified.

One of the great authorities for this period has claimed that "the choice for Ireland in the seventeenth century did not lie between absolutism and Parliamentary control, but between absolutism and anarchy." If this were indeed so—and students of Irish history are almost bound to admit its truth—then Thomas Wentworth, Earl of Strafford, the Viceroy who ruled Ireland under Charles , had the makings of an ideal Governor. Strafford had no qualms about using despotic powers; he ruled the country with an iron hand, forcing the nobility, the Church, and the peasantry, to obey his will. Disregarding the "Graces" promised by his king, he turned out the Catholic landowners in Connaught, and by selling the land obtained money to raise an army ready to subdue Ireland and to help Charles in England. One benefit of absolutism was that, while Strafford reigned, his tyranny alone was to be feared; no subordinates were allowed to crush those beneath them, and this in itself was enough to bring prosperity to a land usually torn by countless feuds. Under his rule Ireland made advances in outward prosperity, commerce and agriculture both became more flourishing, and, though the budding woollen manufacture was crushed in the interests of England, linen was introduced and encouraged by the Viceroy, who brought over weavers from Flanders to instruct the people.

When Strafford fell, being impeached by the English Parliament who secured his execution, no one succeeded him in Ireland with any power to control the Irish people suffering under their countless wrongs. Strafford's firm hand no longer guiding the reins of government, the dispossessed Irish in Ulster suddenly rose in rebellion in the autumn of 1641. So unexpected was their attack that the colonists for a time lay at their mercy, helpless before men from whom all pity had flown in a burning sense of injustice. The numbers of those who perished vary according to the prejudices of the writer, but many thousands undoubtedly died either from the relentless swords of the maddened Irish or from being turned out into the bitter cold of the night stripped of their clothing. When the colonists were able to recover from the first shock, they resisted the rebels and retaliated with fierce cruelty. The rebels had at first been led by Sir Phelim O'Neill, a man of no capacity, but afterwards a relative of Tyrone, Owen Roe O'Neill, took the command, and stopped the indiscriminate bloodshed, for which he declared his abhorrence.

Affairs in England being so unsettled, the Long Parliament preparing to fight the king, no real attempt was made to crush the rebellion, which grew daily. The Anglo-Irish, nearly all Catholics, joined the Irish under Owen Roe O'Neill, and, while still acknowledging King Charles, were determined to protect their religion and their land. The bond of religion was the only thing which held the triumphant Irish forces together, for the Anglo-Irish hated the shameful deeds perpetrated in the early days of the rising by the Celts of Ulster, while the Irishry were simply bent upon ejecting the English colonists. Still, such was the impotence of England at the time that, if there had only been a man of commanding power among the Irish, he might have knit together all the various factions in the country; and, though he might have failed to keep the English out altogether, he could probably have forced such terms that the miseries of the eighteenth century would have been unknown.

Ormond, leading the small Royalist forces, was told by Charles to try to effect terms of peace with the Irish in order to gain their help against the English Parliament; but when the limited toleration of the Catholics —all that Ormond was able to offer—was refused, Ormond himself gave up his command and retired from Ireland. After he left, the Irish began to suffer reverses from the Parliamentary troops, and Ormond was requested by the Royalist English, and most of the combined Irish then in arms, to return and lead them. According to the treaty arranged in January, 1649, Ormond promised, in the King's name, a greater freedom of worship to the Catholics. For a time Ormond's hope of restoring the King's authority seemed likely to be achieved, but all success vanished when Cromwell landed in Ireland in August, with a well-trained army of stern Puritan soldiers. Cromwell had come to fulfill a religious duty—to punish the Catholics for their cruelties during the rising in Ulster. With this in his mind, regarding all Catholics as enemies of God, he carried on a ruthless campaign, offering all the glory to God. At Drogheda and Wexford no quarter was shown, as he himself wrote: "I believe we put to the sword the whole number of the defendents." So great was the terror effected by this stern judicial slaughter—for it was not the thoughtless cruelty of ill-governed soldiers—that town after town surrendered to Cromwell, who proceeded on a conquering march through Ireland. Dissensions were rampant among the Irish, the Protestants under Ormond being hated by the Catholics, who were now indignant that Charles should have proclaimed himself a Presbyterian to please the Scottish people. After Cromwell had returned to England, Ireton continued his work till the war was ended, after eight years of turmoil.

Cromwell looked upon Ireland as a conquered country inhabited by a people for whom one need have no sympathy, as their religion was abominable and anti-Christian. In England, once the war was over, the Royalists were not entirely robbed of their lands, but allowed to return to them in peace. But it was otherwise in unfortunate Ireland. Both Protestants and Catholics had fought against the Parliament, who therefore considered the whole land forfeited to the State. Land was much needed to meet the Government's obligations. The Parliamentarian soldiers were promised land to cover arrears of payment, and land, too, was demanded by those from whom the Government had borrowed money for this war. The method pursued was simple in the extreme. All Catholic land owners were ordered to quit their estates and remove westward to Connaught, leaving their lands to be divided among the new claimants. The peasantry were allowed to remain, but they had to witness the heartrending departure of their masters and mistresses, who by a certain date early in 1654 left the homes of their ancestors for the desolate wilds of Connaught. No wonder such a wholesale confiscation has burned deep into the memories of the Irish people.

Commissioned by Henry Cromwell, the Deputy, a survey of Ireland was made by Dr. Petty, who divided the land among the new owners. As under Strafford, Ireland made outward progress under the peace enforced by Cromwell's stern rule; but it was not a deep-rooted prosperity, being planted upon the sullen despair of the majority of the nation.

Upon the death of Cromwell, the restoration of Charles in Ireland was effected as easily as in England. But though restored to his throne, Charles was faced with many difficulties. Naturally, those who had been with him in exile and those who had fought for his father wanted some reward and the restoration of their estates. But that would mean the forcible ejection of all Cromwell's soldiers, and Charles was not anxious for any more fighting. Ormond regained his land with large accessions, together with a ducal title, and many others who had access to the royal ear managed to obtain their property or grants of land. Most of those who had received their lands from Cromwell remained undisturbed, for a large part of the vast area confiscated under the Commonwealth was still unappropriated. Former Protestant owners and Royalist officers were satisfied after the King had gratified his special friends, and then came the Catholic claims. Whatever the change of English rulers might be, they were united in the policy of maintaining the English Protestant ascendancy, and King Charles, like all the Stuarts, had no special predilection for Ireland. Still, the Catholics had fought and suffered in the Stuart cause, so some attempt had to be made to meet their claims. Each Catholic owner had to satisfy the Judge of the Court of Claims, set up in Dublin, that he had taken no part in the Irish war before 1649, when Ormond had taken command for the King. It was hoped that this provision would exclude many, but far more passed the test than there was land with which to supply them. The Cromwellian colonists were forced to yield a portion of their property, which was then spread out among those Catholics who were considered "innocent," and the rest of the Catholic owners, some 3,000 of whom had never even had their "innocence" tested, were left to do the best they could for themselves. All this apportionment of land was made legal by the Act of Settlement.

During the greater part of this reign Ireland was governed by the Duke of Ormond, a fair-minded and capable ruler. Under his guidance Ireland had a rare interval of peace, during which time the land improved both in agriculture and commerce. Belfast and Dublin grew in population and importance, and the manufacture of wool and linen revived. The prohibition of trading with the colonies brought about by England's Navigation Acts was not felt much at this time, for Ireland was not yet in a condition to establish much overseas commerce.

Ormond was a Protestant, upholding the supremacy of the Anglican Church, which now asserted its authority above all other Protestant forms of worship, as well as over the Catholics. By the Act of Uniformity, enforcing the Prayer-Book, many Presbyterians were obliged to leave Ulster; but the Catholics were permitted greater freedom of worship, though not allowed to hold any office in the State. There was only one Irish Catholic victim to the panic aroused in England by the rumour of a vast Catholic plot, caused by the false evidence of Titus Oates. Dr. Plunkett, Roman Catholic Archbishop of Armagh, suffered death at Tyburn, though quite innocent of the charge of raising a rebellion. But his was the only death at this time, whereas in England many lost their lives through the wild and unreasonable alarm of the Protestants. Indeed, Ireland remained quiescent, while England at the end of Charles's reign, when it was evident that a Catholic King must succeed to the throne, had become full of unrest. But, as it had happened so often before in Ireland, it was only the calm preceding a storm, a storm that was brief in its duration, but which was to usher in a lengthy period of hopeless misery and degradation for almost five-sixths of the Irish people.