In what manner he was said to be connected with the conspiracy, or what was the specific charge brought against him, is nowhere clearly stated; but as Lord Preston—one of the captured messengers—declared he was one of the plotters, and a man of the name of William Fuller swore to the correctness of Preston's statement, the matter assumed a serious aspect. As the origin of the plot was believed to have been among the Catholics, the same misrepresentations of Penn being a Jesuit in disguise were again brought forward, and the passions of the people being much inflamed against the intriguing papists, it was thought a fair trial could not be obtained for him. Under these circumstances, some accounts represent that William Penn voluntarily secluded himself where he could not be easily seen; waiting until a time should arrive when he might have a fair opportunity to clear himself; while others state that, having been examined before the Privy Council, he was ordered to remain a prisoner in his own house, under surveillance. The latter is the more probable, as he could hardly have supposed he could escape the search the government would make for him; especially as he kept up intercourse with his friends. Thus, in the Third month of 1691, he addressed an epistle to the Yearly Meeting in London, in order to remove any unfavorable impression that might have been made in the minds of his brethren by his forced seclusion. In this he says: "My privacy is not because men have sworn truly, but falsely, against me; for wicked men have laid in wait for me, and false witnesses have laid to my charge things that I knew not; who have never sought myself, but the good of all, through great exercises; and have done some good, and would have done more, and hurt to no man; but always desired that truth and righteousness, mercy and peace, might take place among us."

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.

In 1696 William Penn was married to Hannah, the daughter of Thomas Callowhill, of Bristol,—a sober, religious woman, who survived him several years. Soon after this event he sustained an afflictive bereavement in the death of his eldest son, Springett Penn, in the twenty-first year of his age. He was a pious and amiable young man, of whom, in a touching testimony to his worth, William Penn says, "I lost all that any father can lose in a child."

He had been absent from his colony for many years, though longing to return there, and oversee the working of the government he had instituted, and the growth of the prosperous colony he had been a principal means of planting on the shores of the Delaware. But the various troubles in which he had been involved, and the great loss of pecuniary means that had resulted from his outlay for the Province, and the dishonesty of his agent in Ireland, had so crippled and embarrassed him, that he had been unable to carry out his strong desire to cross the Atlantic, and spend the remainder of life amid the Friends and scenes he pictured eminently propitious to secure comfort and peace. But in 1699, having settled his affairs in England and Ireland, so as not to require his personal oversight, in the Seventh month he embarked with his wife and family for Philadelphia, expecting to end his days in the Province. The voyage, providentially, was a long one; occupying three months; by which delay on the ocean they did not arrive in the city until after the malignant fever, of which so many had died, had passed away.

William Penn brought with him certificates from three meetings of Friends in England: one from "The Second-day's Meeting of Ministering Friends" in London; one from the "Men's Meeting of Friends" in Bristol, where he had resided for some years, and another from "A Monthly Meeting held at Horsham;" all expressing their full unity with and love for him as a member and minister. The reception of these certificates is recorded on the minutes of the Monthly Meeting of Friends, of Philadelphia.

The arrival of the Proprietor, after an absence of fifteen years, was hailed with joy by the people generally, and doubtless he supposed that he could now pass his days in usefulness and tranquillity. But William Penn soon found that troubles beset him on every hand, and that his wise counsels and cherished plans of improvement were thwarted and opposed by a faction bent upon promoting their own selfish schemes and interests.

A circumstance now occurred which separated him from his American possessions forever. A bill had been introduced into Parliament for changing the colonial into regal government. This measure, if adopted, would take the control of the colony out of his hands, and substitute military rule for the mild and pacific government he had established. From a sense of duty, although very reluctantly, he yielded to the request of his friends in England, that he would immediately return thither.

The news of his intended departure was received by the inhabitants with feelings of sincere regret. Perhaps none felt it more deeply than the aborigines. On this occasion, a number of them waited upon him at his residence at Pennsbury. The interview was conducted with great gravity. One of the chiefs, in the course of his remarks, said "that they never first broke their covenants with any people;" striking his hand upon his head, he said "they did not make them there, but"—placing it upon his breast—"they made them there."

William Penn sailed for England in the Eighth month, 1701, having been in the Province about two years. On the eve of his departure he presented Philadelphia with a charter, constituting it a city.

The bill to change the form of the colonial government was never passed into a law, but other engagements prevented his return to Pennsylvania. In 1705, in a brief but forcible epistle to Friends, he exhorts them to hold all their meetings in that which set them up, the heavenly power of God. In 1706 he removed with his family to Brentford, about eight miles from London. In 1709 he went forth on a gospel mission through the western parts of England, which was his last journey of this kind. In 1710 he removed to Rushcomb, in Buckinghamshire, where he continued to reside until his death. In 1712 he had three attacks of apoplexy. By these his mental powers were so weakened that he was rendered incapable of transacting business. In this situation he remained for several years, without much bodily suffering, and appeared to enjoy great quietness and sweetness of mind. In the latter part of 1714 he was visited by Thomas Story, who says of him, "that he had a clear sense of truth, was plain, by some very clear sentences he spoke in the life and power of Truth, in an evening meeting we had there; wherein we were greatly comforted, so that I am ready to think this was a sort of sequestration of him from all the concerns of this life, which so much oppressed him, not in judgement but in mercy, that he might not be oppressed thereby to the end."