During his retirement he employed his pen diligently, producing several works of much value. The refusal of Friends in Pennsylvania to contribute money for the erection of forts or other military purposes, had given great offence to the home government, and the enemies of Penn took advantage of this, and of the position he was now in, with charges of treason hanging over him, to obtain an order from the King and Council, in the early part of 1692, to annex the government of Pennsylvania to that of New York, then presided over by Colonel Fletcher. Penn remained shut out from the world, and deprived of opportunity to serve the cause of truth and righteousness, and his brethren of the same faith, except by his pen, for more than two years; his character stained in the estimation of some, and his valuable services forgotten by many others, who, perhaps, thought he had indeed fallen to rise no more. But there were men of eminence who had never believed William Penn guilty of the crime laid to his charge, and were awaiting the right opportunity to have justice done to his position and character. Among these was the celebrated John Locke, who esteemed him, not only as a man of exalted virtue and great literary attainment, but as a personal friend. He applied to King William for a pardon; but William Penn was too conscious of innocence, and too fully persuaded that in due time his innocence would be made manifest to the world, to be willing to accept of any release that would imply he had been guilty. In the meantime, Lord Preston, who had made the charge against him, had fled the country, and Fuller, his witness, having been detected in perjury, was, by order of Parliament, tried as an imposter, in the Court of the King's Bench, found guilty, and sentenced to stand in the pillory. Lords Ranelagh, Rochester, and Sidney now waited on the King, and, stating that the name of William Penn had never been found in any of the letters or papers connected with the conspiracy, and that the charge against him rested solely on the accusation of two men who were known to be unworthy of belief, urged upon him the injustice and hardship of his case. The King appears to have heard them patiently, and replied that William Penn was an old acquaintance of his; that he had nothing to allege against him, and that he might follow his business as freely as ever. Afterwards the King gave an order to the principal Secretary of State for his freedom; which was communicated to him in the presence of the Marquis of Winchester. He, however, sought and obtained a hearing before the Privy Council; and, after a full examination of the charges, he was honorably acquitted. The cloud that had long obscured his standing and services was now dispelled, and he returned to his family and friends, to resume the position he had before attained in the church, and in civil society. His wife survived his release but little more than two months.