This was a hard change for William Penn, and he seems to have done nothing to make it easier. There were courtiers who passed with incredible swiftness from one allegiance to the other; he was not among them. Others fled to France, but he stayed. He was arrested. In his examination before the Privy Council he declared that he "had done nothing but what he could answer for before God and all the princes in the world; that he loved his country and the Protestant religion above his life, and had never acted against either; that all he had ever aimed at in his public endeavors was none other than what the king had declared for [religious liberty]; that King James had always been his friend, and his father's friend, and that in gratitude he himself was the king's, and did ever, as much as in him lay, influence him to his true interest." Penn was released.
The new king began his reign with the Toleration Act, which Parliament passed in 1688, and from which dates the establishment of actual and abiding religious liberty in England. Thus Penn's great purpose was accomplished by one with whom he was not in accord. Sometimes a political party adopts the projects for which its opponents have long labored, and carries them out even more vigorously than they had been planned originally. The initial reformers are glad that their ideals have been realized, but their zeal must be uncommonly impersonal if the success brings them quite so much joy as it logically ought. It is not likely that the Toleration Act filled the soul of William Penn with great jubilation. Indeed, we know that he insisted to the end of his life that James, if he had been let alone, would have done all that William did, and more too, and better.
The years which followed were full of trouble. Macaulay says that in 1689 Penn was plotting against the government; but the evidence does not suffice to establish the fact. The Privy Council, in 1690, confronted Penn with an intercepted letter to him from James, asking for help. But, as Penn said, he could not hinder the king from writing to him. He added, however, with characteristic boldness, that since he had loved King James in his prosperity he should not hate him in his adversity. He was again discharged.
In that same year, however, James invaded Ireland, and the situation of his friends in England was thereby made increasingly difficult. Penn was arrested with others, and in prison awaited trial for several months. The result was as before,—he was found in no offense. But before a month had passed, he learned that another warrant was out against his liberty. Officers went to take him at the funeral of George Fox, but arrived too late. By this time he had concluded that the path of prudence was that which led into a wise retirement. He hid himself for the space of three years. He was publicly proclaimed a traitor, and was deprived of the government of his colony. He was "hunted up and down," he says, "and could never be allowed to live quietly in city or country."
Finally, the government were persuaded either that Penn was innocent, or that no further danger was to be apprehended from him, and several noblemen, interceding with the king, procured his pardon. They represented his case, he says, as not only hard, but oppressive, there being no evidence but what "impostors, or those that fled, or that have since their pardon refused to verify (and asked me pardon for saying what they did) alleged against me." The king announced that Penn was his old acquaintance, and that he might follow his business as freely as ever, and that for his part he had nothing to say to him.
Thus again, and at last, the political accusations against William Penn came to nothing. He had been in a hard position as the faithful friend of a dethroned monarch in a day when conspiracies were being made on every hand. That he should have been suspected of treason was inevitable. That in his unconcealed affection for James and disapproval of William he said imprudent things is likely enough. Prudence was not one of his virtues. He was never calculatingly careful of his own welfare. But that he was ever untrue to William, or did any act, or consented to any, which could reasonably be called treacherous, is not only quite unproved, but is out of accord with the true William Penn as he is revealed in his writings and in all his life. The only fault which has been clearly established against him is that of liking James better than he liked William. He was a stanch friend to his friend; that is the sum of his offending, wherein the only serious regret is that his friend was not more worthy of his steadfast and unselfish friendship. "At no time in his life," says Mr. Fiske, "does he seem more honest, brave, and lovable, than during the years, so full of trouble for him, that intervened between the accession of James and the accession of Anne."