At daybreak they fell on their hosts, and in a few moments thirty of the clansfolk lay dead on the snow. The rest, sheltered by a storm, escaped to the mountains to perish for the most part of cold and hunger. "The only thing I regret," said the Master of Stair when the news reached him, "is that any got away." Whatever horror the Massacre of Glencoe has roused in later days, few save Dalrymple knew of it at the time. The peace of the Highlands enabled the work of reorganization to go on quietly at Edinburgh. In accepting the Claim of Right with its repudiation of Prelacy, William had in effect restored the Presbyterian Church, and its restoration was accompanied by the revival of the Westminster Confession as a standard of faith, and by the passing of an Act which abolished lay patronage. Against the Toleration Act which the King proposed, the Scotch Parliament stood firm. But the King was as firm in his purpose as the Parliament. So long as he reigned, William declared in memorable words, there should be no persecution for conscience' sake. "We never could be of that mind that violence was suited to the advancing of true religion, nor do we intend that our authority shall ever be a tool to the irregular passions of any party".

It was not in Scotland, however, but in Ireland that James and Lewis hoped to arrest William's progress. In the middle of his reign, when his chief aim was to provide against the renewed depression of his fellow religionists at his death by any Protestant successor, James had resolved (if we may trust the statement of the French ambassador) to place Ireland in such a position of independence that she might serve as a refuge for his Catholic subjects. Lord Clarendon was dismissed from the Lord-Lieutenancy and succeeded in the charge of the island by the Catholic Earl of Tyrconnell. The new governor, who was raised to a dukedom, went roughly to work. Every Englishman was turned out of office. Every Judge, every Privy Councillor, every Mayor and Alderman of a borough was required to be a Catholic and an Irishman. The Irish army, raised to the number of fifty thousand men and purged of its Protestant soldiers, was entrusted to Catholic officers. In a few months the English ascendency was overthrown, and the life and fortune of the English settlers were at the mercy of the natives on whom they had trampled since Cromwell's day. The King's flight and the agitation among the native Irish at the news spread panic therefore through the island.

Another massacre was believed to be at hand; and fifteen hundred Protestant families, chiefly from the south, fled in terror over sea. The Protestants of the north on the other hand drew together at Enniskillen and Londonderry, and prepared for self-defence. The outbreak however was still delayed, and for two months Tyrconnell intrigued with William's Government. But his aim was simply to gain time. He was in fact inviting James to return to Ireland, and at the news of his coming with officers, ammunition, and a supply of money provided by the French King, Tyrconnell threw off the mask. A flag was hoisted over Dublin Castle, with the words embroidered on its folds "Now or Never." The signal called every Catholic to arms. The maddened natives flung themselves on the plunder which their masters had left, and in a few weeks havoc was done, the French envoy told Lewis, which it would take years to repair. Meanwhile James sailed from France to Kinsale. His aim was to carry out an invasion of England with the fifty thousand men that Tyrconnell was said to have at his disposal. But his hopes were ruined by the war of races which had broken out. To Tyrconnell and the Irish leaders the King's plans were utterly distasteful.

Their policy was that of Ireland for the Irish, and the first step was to drive out the Englishmen who still stood at bay in Ulster. Half of Tyrconnell's army therefore had been sent against Londonderry, where the bulk of the fugitives found shelter behind a weak wall, manned by a few old guns, and destitute even of a ditch. But the seven thousand desperate Englishmen behind the wall made up for its weakness. So fierce were their sallies, so crushing the repulse of his attack, that the King's general, Hamilton, at last turned the siege into a blockade. The Protestants died of hunger in the streets, and of the fever which comes of hunger, but the cry of the town was still "No Surrender." The siege had lasted a hundred and five days, and only two days' food remained in Londonderry, when on the 28th of July an English ship broke the boom across the river, and the besiegers sullenly withdrew. Their defeat was turned into a rout by the men of Enniskillen, who struggled through a bog to charge an Irish force of double their number at Newtown Butler, and drove horse and foot before them in a panic which soon spread through Hamilton's whole army. The routed soldiers fell back on Dublin, where James lay helpless in the hands of the frenzied Parliament which he had summoned.

Every member returned was an Irishman and a Catholic, and their one aim was to undo the successive confiscations which had given the soil to English settlers and to get back Ireland for the Irish. The Act of Settlement on which all title to property rested was at once repealed in spite of the King's reluctance. Three thousand Protestants of name and fortune were massed together in the hugest Bill of Attainder which the world has seen. In spite of James's promise of religious freedom, the Protestant clergy were driven from their parsonages, Fellows and scholars were turned out of Trinity College, and the French envoy, the Count of Avaux, dared even to propose that if any Protestant rising took place on the English descent, as was expected, it should be met by a general massacre of the Protestants who still lingered in the districts which had submitted to James. To his credit the King shrank horror-struck from the proposal. " I cannot be so cruel," he said, "as to cut their throats while they live peaceably under my government." " Mercy to Protestants," was the cold reply, "is cruelty to Catholics".