But 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 to which nine-tenths of the Lowland Scotchmen clung, 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 though the measure failed 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. Ireland had long been the object of special attention on the part of James. 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, he 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. It was with a view to the success of this design that 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 at this very moment indeed inviting James to return to Ireland, and assuring him of his fidelity. To James this call promised the aid of an army which would enable him to help the Scotch rising and to effect a landing in England, while Lewis saw in it the means of diverting William from giving effectual aid to the Grand Alliance. A staff of French officers with arms, ammunition, and a supply of money was placed therefore at the service of the exiled king, and the news of his coming no sooner reached Dublin at the opening of 1689 than 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 Irishmen 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.