At no time had the Church been so strong or so popular as at the Revolution, and the reconciliation of the Nonconformists would have doubled its strength. It is doubtful whether the disinclination to all political change which has characterized it during the last two hundred years would have been affected by such a change; but it is certain that the power of opposition which it has wielded would have been enormously increased. As it was, the Toleration Act established a group of religious bodies whose religious opposition to the Church forced them to support the measures of progress which the Church opposed. With religious forces on the one side and on the other England has escaped the great stumbling-block in the way of nations where the cause of religion has become identified with that of political reaction. A secession from within its own ranks weakened the Church still more. The doctrine of Divine Right had a strong hold on the body of the clergy, though they had been driven from their other favourite doctrine of passive obedience, and the requirement of the oath of allegiance to the new sovereigns from all persons in public functions was resented as an intolerable wrong by almost every parson.

Sancroft, the Archbishop of Canterbury, with a few prelates and a large number of the higher clergy, absolutely refused the oath, treated all who took it as schismatics, and on their deprivation by Act of Parliament regarded themselves and their adherents, who were known as Nonjurors, as the only members of the true Church of England. The bulk of the clergy-bowed to necessity, but their bitterness against the new Government was fanned into a flame by the religious policy announced in this assertion of the supremacy of Parliament over the Church, and the deposition of bishops by an act of the legislature. The new prelates, such as Tillotson, the Archbishop of Canterbury, and Burnet, Bishop of Salisbury, were men of learning and piety; but it was only among Whigs and Latitudinarians that William and his successors could find friends among the clergy, and it was mainly to these that they were driven to entrust the higher offices of the Church. The result was a severance between the higher dignitaries and the mass of the clergy which broke the strength of the Church; and till the time of George the Third its fiercest strife was waged within its own ranks.

But the resentment at the measure which brought this strife about already added to the difficulties which William had to encounter.

Yet greater difficulties arose from the temper of his Parliament. In the Commons the bulk of the members were Whigs, and their first aim was to redress the wrongs which the Whig party had suffered during the last two reigns. The attainder of Lord Russell was reversed. The judgements against Sidney, Cornish, and Alice Lisle were annulled. In spite of the opinion of the judges that the sentence on Titus Oates had been against law, the Lords refused to reverse it, but even Oates received a pardon and a pension. The Whigs however wanted not merely the redress of wrongs but the punishment of the wrong-doers. Whig and Tory had been united, indeed, by the tyranny of James; both parties had shared in the Revolution, and William had striven to prolong their union by joining the leaders of both in his first Ministry. He named the Tory Earl of Danby Lord President, made the Whig Earl of Shrewsbury Secretary of State, and gave the Privy Seal to Lord Halifax, a trimmer between the one party and the other. But save in a moment of common oppression or common danger union was impossible. The Whigs clamoured for the punishment of Tories who had joined in the illegal acts of Charles and of James, and refused to pass the Bill of General Indemnity which William laid before them.

William on the other hand was resolved that no bloodshed or proscription should follow the revolution which had placed him on the throne. His temper was averse from persecution; he had no great love for either of the battling parties; and above all he saw that internal strife would be fatal to the effective prosecution of the war. While the cares of his new throne were chaining him to England, the confederacy of which he was the guiding spirit was proving too slow and too loosely compacted to cope with the swift and resolute movements of France. The armies of Lewis had fallen back within their own borders, but only to turn fiercely at bay. Even the junction of the English and Dutch fleets failed to assure them the mastery of the seas. The English navy was paralyzed by the corruption which prevailed in the public service, as well as by the sloth and incapacity of its commander. The services of Admiral Herbert at the Revolution had been rewarded by the Earldom of Torrington and the command of the fleet; but his indolence suffered the seas to be swept by French privateers, and his want of seamanship was shown in an indecisive engagement with a French squadron in Bantry Bay. Meanwhile Lewis was straining every nerve to win the command of the Channel; the French dockyards were turning out ship after ship, and the galleys of the Mediterranean fleet were brought round to reinforce the fleet at Brest. A French victory off the English coast would have brought serious political danger, for the reaction of popular feeling which had begun in favour of James had been increased by the pressure of the war, by the taxation, by the expulsion of the Non-jurors and the discontent of the clergy, by the panic of the Tories at the spirit of vengeance which broke out among the triumphant Whigs, and above all by the presence of James in Ireland. A new party, that of the Jacobites or adherents of King James, was just forming; and it was feared that a Jacobite rising would follow the appearance of a French fleet on the coast.

In such a state of affairs William judged rightly that to yield to the Whig thirst for vengeance would have been to ruin his cause. He dissolved the Parliament, which had refused to pass a Bill of Indemnity for all political offences, and called a new one to meet in March. The result of the election proved that he had only expressed the general temper of the nation. The boroughs had been alienated from the Whigs by their refusal to pass the Indemnity, and their attempts to secure the Corporations for their own party; while in the counties parson after parson led his flock to the poll against the Whigs. In the new Parliament the bulk of the members proved Tories. William accepted the resignation of the more violent Whigs among his councillors, and placed Danby at the head of affairs. In May the Houses gave their assent to the Act of Grace. The King's aim in this sudden change of front was not only to meet the change in the national spirit, but to secure a momentary lull in English faction which would suffer him to strike at the rebellion in Ireland. While James was King in Dublin it was hopeless to crush treason at home; and so urgent was the danger, so precious every moment in the present juncture of affairs, that William could trust no one to bring the work as sharply to an end as was needful save himself.