Richard Talbot, made Duke of Tyrconnel by , his personal friend, entered upon his duties as Lord Deputy in 1687, having previously acted as commander of the army. He was the first Catholic to hold that position since Henry had thrown over the jurisdiction of the Pope, and he lost no time in showing to the Protestants that a complete change was to be instituted. Catholics were at once admitted wholesale to offices of trust. Catholic judges and magistrates were appointed, and Catholic officers superseded the Protestant ones in the army. Not only that, but Tyrconnel took upon himself to disregard the Act of Settlement, though James had declared he would maintain it. The old owners began clamouring for and seizing their lands till the Protestants were in a state of alarm. Many hastened to England, while others took refuge in Ulster, flocking to Enniskillen and Londonderry, two Protestant strongholds. Tyrconnel had made a serious mistake in removing the garrison from Londonderry, leaving the Protestants at liberty to declare for William when James was driven from his throne.

James fled precipitately from his triumphant son-in-law, and was warmly received in France by Louis , glad of any opportunity to annoy his old-time enemy, William of Orange. Provided with French money, officers, and ammunition, but with no army, James entered Ireland in the spring of 1689. The Irish flocked enthusiastically to his standard, finding in it a rallying-point round which to fight for their country. All the way from Cork to Dublin the people lined the road, welcoming their King with flowers, while Dublin bedecked itself for the royal entry. James found himself at the head of a large army, composed of all the Catholics of Ireland, but it was an army lacking in discipline and ill-supplied with arms. The cavalry, formed largely of Irish gentlemen, was the only efficient part which was able to render a good account of itself at the Battle of the Boyne. Though not devotedly attached to the Stuart cause, the Irish were intensely eager to fight under Catholic leaders for their faith and their land, the priests proclaiming it as a holy war.

Money was soon wanting, the French supplies having rapidly evaporated. To meet this want, James issued a base coinage which caused ruin to those who were forced to accept it, and which was of no use for purchasing ammunition from abroad. From the very beginning there were signs of disunion in the army. James and his English followers were only using the Irish as a means to regain England, the French lent aid to embarrass William , while the Irish themselves would have liked James to remain a king in Ireland.

Soon after his arrival in Dublin, James set off with the army to force the people of Londonderry to open their gates, a task which was expected to be an easy one. Though Lundy, the Governor, had deserted to the enemy, the townsfolk of Derry would hear no word of surrender, and soon were enrolled as defenders of the walls, which were regarded by the assailants with contempt. Seven thousand men were mustered and apportioned their duties, carrying them out with strict obedience. Protestants of English or Scottish blood, they were determined to hold their city against the Popish idolaters, as they regarded the Irish. For nearly three and a half months they held out against forces and extreme depths of starvation. When an assault had been repulsed James retired, leaving the command to Rosen, a French general, who had recourse to any barbarity in order to reduce the city to submission. A boom was placed across the river and a severe blockade maintained, so that no food was able to reach the besieged, who were reduced to eating horses and dogs and hunting for rats. All provisions were searched for and doled out to the inhabitants.

On June 15 great excitement reigned in the city when ships were discovered in the bay, and a message was obtained saying that they contained the longed-for help from England—soldiers, food, and ammunition. But Kirke, the commander of the little fleet, thought it impossible to relieve Derry, and so drew off, leaving the city to its fate. Even then the brave citizens would not give way, though pestilence broke out owing to the bad food, and the men who were left to man the walls had grown haggard and weak. At last, six weeks after they had first seen the relief ships, help came to the despairing city. Owing to a direct command, Kirke made an effort to break the boom across the river. In the words of Lord Macaulay, whose story of the gallant defence can never be surpassed, we read of the eventful evening of July 28: "The sun had just set; the evening sermon in the cathedral was over; and the heart-broken congregation had separated; when the sentinels on the tower saw the sails of three vessels Dartmouth, a small ship-of-war with thirty guns, and two merchantmen, the Mountjoy  and the Phœnix.")?> coming up the Foyle. . . . Then the Mountjoy  took the lead, and went right at the boom. The huge barricade cracked and gave way; but the shock was such that the Mountjoy  rebounded and stuck in the mud. A yell of triumph rose from the banks: the Irish rushed to their boats, and were preparing to board; but the Dartmouth  poured on them a well-directed broadside, which threw them into disorder. Just then the Phœnix  dashed at the breach which the Mountjoy  had made, and was in a moment within the fence. Meantime the tide was rising fast. The Mountjoy  began to move, and soon passed safe through the broken stakes and floating spars." Late that evening the starving defenders were indulging in a full meal of beef and flour and pease, and three days later the Irish army were in full retreat.

Meanwhile James had summoned a Parliament to Dublin, which consisted almost entirely of Catholics, many of whom were men of birth and distinction. This Parliament has been denounced by some writers as grossly unjust in its actions, and by others as the only patriotic Parliament that had assembled for centuries. As a matter of fact, it was a fair counterpart of the contemporary Parliaments of England and Scotland. Having power in its hands, it naturally repealed the unfair Act of Settlement and tried to cancel Poynings' Act; but, though passed by both Houses, James never actually signed the repeal of the latter. Full religious liberty was announced, and a fair adjustment made of Church property between the Catholics and Protestants. So far there is nothing much to complain of their actions, but they proceeded to pass what Mr. Green pronounces to be "the hugest Bill of Attainder the world has seen," on 2,500 absent people, unless they produced themselves on a certain day.

William of Orange had been so occupied in England that, beyond despatching relief to Londonderry, he had done little towards fighting James in Ireland. But in the autumn he sent off the Duke of Schomberg, one of his most tried generals, with a large army. Schomberg, who was getting an old man, did not attempt a forced march upon Dublin, but went into winter-quarters at Dundalk, where his army dwindled rapidly under the fatal influence of the Irish climate. James, reinforced by some 6,000 French troops in exchange for an equal number of Irish soldiers, also remained inactive during the winter.

The following June William arrived in person, commanding an army of 37,000 men, composed of all the various races of Europe. Making no delays, he marched from Carrickfergus, where he had landed, towards Dublin, meeting James's army at the River Boyne, about thirty miles north of Dublin. The wide river protected the Irish army in front, but William sent a troop under Schomberg's son to cross a bridge higher up, and so reach the left wing of the enemy. The only retreat for the Irish lay through a narrow pass which, if taken by the enemy, would mean destruction for the whole army. The French troops were sent to hold this road, removing a steadying influence from the untrained Irish infantry, who broke at the attack of the English. But for a time William's forces were held at bay by the Irish cavalry under Richard Hamilton, until their leader was captured and many hundreds of them had fallen. James had taken no part in the battle, upon which his fortunes depended, and when he saw which way it was going he fled back to Dublin, greeting, so the saying goes, Tyrconnel's wife with, "Madam, your countrymen have run away." "If they have, sire," she replied, "your Majesty seems to have won the race." The next morning the army flocked into Dublin; but, though he could still have made a good stand, James was seized with panic, declared he would never command an Irish army again, and hurried to Waterford, where he took ship for France.

Though the King for whom they were nominally fighting had cowardly fled from the scene of action, the Irish troops still held out, even in face of William's offer of free pardon to those who would submit. Gathering round Limerick, the Irish, under Patrick Sarsfield, determined to hold the city and redeem their honour. The French commander, who was weary of the war, opposed the attempt, saying angrily that the place was so weak that it could be taken with roasted apples. But, feeble as were its outward defences, the story of its siege shows, as Macaulay points out, what religious and patriotic enthusiasm can do even against apparently hopeless odds. In great disgust the French retreated to Galway, leaving Sarsfield to conduct the siege. Sarsfield stands out as the hero of the war, a man of courage, resource, and honour, "a gentleman," as Macaulay writes, "of eminent merit, brave, upright, honourable, careful of his men in quarters, and certain to be always found at their head in the day of battle." Having done his utmost to provision the city and to repair its defences, Sarsfield was ready for William, who arrived in the middle of August. By good fortune Sarsfield heard of the expected arrival of a train of siege-guns to join William's army. Getting secretly out of the town, Sarsfield succeeded in intercepting and defeating this convoy, blowing up their guns, and returning safely to Limerick. This gallant deed hindered the siege, but, having repaired two of the damaged guns, William managed to make a breach in the walls, and followed it up by a general assault. But the desperate courage of the defenders drove back the English troops, and autumn coming on, when the rain and the rising river would make the low-lying ground a deadly fever-bed, decided William to raise the siege. He himself returned to England, leaving Ginkel in command.

In the summer of 1691 the last battles were fought by the Irish against William's veterans, commanded by Ginkel. St. Ruth, a French general, now lead the Irish, with Sarsfield as his second in command, and, unfortunately, the two men did not agree. Owing to their lack of concord, the English managed to take Athlone and cross the Shannon there, and also to inflict a crushing defeat at Aughrim in Galway, where St. Ruth was killed. The last episode of the war took place at Limerick, which underwent a second siege. The approach of autumn made Ginkel open to terms, and Sarsfield was ready to negotiate while he was still at the head of an army. The Treaty of Limerick was signed by the two generals and the Lords Justices. According to its terms, the Irish army was to retire with full honours and with permission to enlist in foreign service. A limited toleration secured for the Catholics "such privileges in the exercise of their religion as were consistent with the laws of Ireland, or as they did enjoy in the reign of Charles "; also the inhabitants of Limerick, the officers and soldiers of the Irish army in five particular counties, and all "persons under their protection  in the said counties," were to receive full pardon and the retention of their estates. The vast majority of the Irish soldiers enlisted in the French army, their departure from their native country being the occasion of heartrending scenes when they said farewell to their mothers and wives and children. Through intention or error, the words in italics of the treaty were left out, and, though King William declared that it was a mistake, the Protestant Irish Parliament refused to accord this favour to Irish land-owners, whom they regarded as a conquered enemy, and their land as legitimate booty.

Convinced by the brief reign of the Catholics in 1689 that it was not safe to admit them to any power, the Parliament proceeded to pass a series of laws calculated to crush and degrade most of the inhabitants of the country. Catholic landowners now retained only one-eighth of the land of Ireland, and, in order to prevent their obtaining any further hold, no Irish Catholic was allowed to purchase land, but only to hold a short leasehold. With the idea of breaking up the estates, a Catholic father had to portion out his property among his various children. Not only that, but if the eldest son proclaimed himself a Protestant, he obtained the entire property, an encouragement to family dissensions. Should a wife or younger child desert the Catholic faith, they could at once claim a separate share of the parental estates and an entire freedom from parental control. Deprived of all share in the government of the country, no longer being allowed to sit in Parliament or to exercise a vote, the Catholics were also unable to enter the army or navy, to become magistrates or barristers, or to sit on juries. Catholic orphans had to be brought up by Protestant guardians, and there were no schools in which a Catholic child could be educated. No Catholic could wear any weapon or possess a horse of a greater value than £5. Intermarriage between Catholic and Protestant was rendered almost impossible. It seems to have been thought that by this method of treatment—the humiliation of a whole nation—the Catholics would either disappear or become Protestant. The Catholic Church services were not entirely forbidden, but none of the higher dignitaries of the Church were allowed to live in Ireland, and the village priests were obliged to register themselves and to take an oath impossible for any Catholic. Is it any wonder that Edmund Burke should write of this code of penal laws as "a machine of wise and elaborate contrivance, and as well fitted for the oppression, impoverishment and degradation of a people, and the debasement in them of human nature itself, as ever proceeded from the perverted ingenuity of man"?

As a natural consequence of this legislation, "the most complete code of persecution that ingenious bigotry ever compiled," Ireland suffered in prosperity. The Catholic gentry, outcast from all social duties and pleasures, sank into lethargy and sloth, having no natural outlet for their energies; while the Catholic peasantry were in a condition bordering on famine, ground down by the Protestant middlemen who managed the estates of the absentee owners. The Protestant minority suffered from the poverty of the Catholics, whom they treated with harshness and insolence. It seems almost incredible that, at a time removed by more than a century from the fighting period of Protestantism, the Irish Protestants should have disgraced themselves by such a mean and despicable code of laws, spoken of by Lord Macartney, Irish Secretary in 1769, as "the harsh dictates of persecution, not the calm suggestion of reason and policy." No doubt Macartney was right when he suggested that the operative cause of the persecution was the desire to maintain the lands of the Catholics, only possible when they were rendered politically and socially impotent.

One happy result only came about from the Penal Code, and that was unforeseen. The Catholic Church rose triumphant through its hour of trial. Its priests, often only ignorant men drawn from the upper classes of the peasantry, were so full of fervent piety, and lived such virtuous lives of devoted service, that they won the glorious crown of a people reclaimed from vice. Ireland stands high to-day as one of the purest-living nations of Europe.

When the seventeenth century drew to its close Ireland was a thoroughly conquered country, and for nearly a hundred years there was no stirring among the people. But the foundations of the peace had not been well and truly laid.