William then spent nearly a year in Ireland, administering his father's estates. When he returned, in 1670, he found his Quaker [brethren] in greater trouble than before. In that perilous season of plots and rumors of plots, when Protestants lived in dread of Roman Catholics, and Churchmen knew not at what moment the Puritans might again repeat the tragedies of the Commonwealth, neither church nor state dared to take risks. The reigns of Mary and of Cromwell were so recent an experience, the Papists and the Presbyterians were so many and so hostile, that it seemed unsafe to permit the assembling of persons concerning whose intentions there could be any doubt. Any company might undertake a conspiracy. The result of this feeling on the part of both the civil and the ecclesiastical authorities was a series of ordinances, reasonable enough under the circumstances, and perhaps necessary, but which made life hard for such stout and frank dissenters as the Quakers. At the time of Penn's return from Ireland, it had been determined to enforce the Conventicle Act, which prohibited all religious meetings except those of the Church of England. There was, therefore, a general arresting of these suspicious friends of Penn's. In the middle of the summer Penn himself was arrested.

The young preacher had gone to a meeting-house of the Quakers in Gracechurch or Gracious Street, in London, and had found the door shut, and a file of soldiers barring the way. The congregation thereupon held a meeting in the street, keeping their customary silence until some one should be moved to speak. It was not long before the spirit moved Penn. He was immediately arrested, and William Mead, a linen draper, with him, and the two were brought before the mayor. The charge was that they "unlawfully and tumultuously did assemble and congregate themselves together to the disturbance of the king's peace and to the great terror and disturbance of many of his liege people and subjects." They were committed as rioters and sent to await trial at the sign of the Black Dog, in Newgate Market.

At the trial Penn entered the court-room wearing his hat. A constable promptly pulled it off, and was ordered by the judge to replace it in order that he might fine the Quaker forty marks for keeping it on. Thus the proceedings appropriately began. William tried in vain to learn the terms of the law under which he was arrested, maintaining that he was innocent of any illegal act. Finally, after an absurd and unjust hearing, the jury, who appreciated the situation, brought in a verdict of "guilty of speaking in Gracious Street." The judges refused to accept the verdict, and kept the jury without food or drink for two days, trying to make them say, "guilty of speaking in Gracious Street to an unlawful assembly." At last the jury brought in a formal verdict of "not guilty," which the court was compelled to accept. Thereupon the judges fined every juryman forty marks for contempt of court; and Penn and the jurors, refusing to pay their fines, were all imprisoned in Newgate. The Court of Common Pleas presently reversed the judges' decision and released the jury. Penn was also released, against his own protest, by the payment of his fine by his father.

The admiral was in his last sickness. He was weary, he said, of the world. It had not proved, after all, to be a satisfactory world. He did not grieve now that his son had renounced it. At the same time, he could not help but feel that the friendship of the world was a valuable possession; and he had therefore requested his patron, the Duke of York, to be his son's friend. Both the duke and the king had promised their good counsel and protection. Thus "with a gentle and even gale," as it says on his tombstone, "in much peace, [he] arrived and anchored in his last and best port, at Wanstead in the county of Essex, the 16th of September, 1670, being then but forty-nine years and four months old."

The admiral's death left his son with an annual income of about fifteen hundred pounds. This wealth, however, made no stay in his Quaker zeal. Before the year was ended, he was again in prison.

Sir John Robinson, the lieutenant of the Tower, had been one of the judges in the affair of Gracious Street. He had either taken a dislike to Penn, or else was deeply impressed with the conviction that the young Quaker was a peril to the state. Finding that there was to be a meeting in Wheeler Street, at which William was expected, he sent soldiers and had him arrested. They conveyed him to the Tower, where he was examined. "I vow, Mr. Penn," said Sir John, "I am sorry for you; you are an ingenious gentleman, all the world must allow you, and do allow you, that; and you have a plentiful estate; why should you render yourself unhappy by associating with such a simple people?" That was the suspicious fact. Men in Robinson's position could not understand why Penn should join his fortunes with those of people so different from himself, poor, ignorant, and obscure, unless there were some hidden motive. He must be either a political conspirator, or, as many said, a Jesuit in disguise, which amounted to the same thing. "You do nothing," said Sir John, "but stir up the people to sedition." He required him to take an oath "that it is not lawful, upon any pretense whatsoever, to take arms against the king, and that [he] would not endeavour any alteration of government either in church or state." Penn would not swear. He was therefore sentenced for six months to Newgate. "I wish you wiser," said Robinson. "And I wish thee better," retorted Penn. "Send a corporal," said the lieutenant, "with a file of musqueteers along with him." "No, no," broke in Penn, "send thy lacquey; I know the way to Newgate."

William continued in prison during the entire period of his sentence, at first in a room for which he paid the jailers, then, by his own choice, with his fellow Quakers in the "common stinking jail." Even here, however, he managed, as before, to write; and he must have had access to books, for what he wrote could not have been composed without sight of the authors from whom he quoted. The most important of his writings at this time was "The Great Case of Liberty of Conscience once more briefly Debated and Defended by the Authority of Reason, Scripture and Antiquity."

Being released from prison, Penn set out for the Continent, where he traveled in Germany and Holland, holding meetings as opportunity offered, and regaining such strength of body as he may have lost amidst the rigors of confinement.

In 1672, being now back in England, and having reached the age of twenty-seven years, he married Gulielma Maria Springett, a young and charming Quakeress. Guli Springett's father had died when [she] was but twenty-three years old, after such valiant service on the Parliamentary side in the civil war that he had been knighted by the Speaker of the House of Commons. Her mother, thus bereft, had married Isaac Pennington, a quiet country gentleman, in whose company, after some search for satisfaction in religion, she had become a Quaker. Pennington's Quakerism, together with the sufferings which it brought upon him, had made him known to Penn. It was to him that Penn had written, three years before, to describe the death of Thomas Loe. "Taking me by the hand," said William, "he spoke thus: 'Dear heart, bear thy cross, stand faithful for God, and bear thy testimony in thy day and generation; and God will give thee an eternal crown of glory, that none shall ever take from thee. There is not another way. Bear thy cross. Stand faithful for God.'"

It was in Pennington's house that Thomas Ellwood lived, as tutor to Guli and the other children, to whom one day in 1655 had come his friend John Milton, bringing a manuscript for him to read. "He asked me how I liked it, and what I thought of it, which I modestly but freely told him; and after some further discourse about it, I pleasantly said to him, Thou hast said much here of Paradise Lost, but what hast thou to say about Paradise found?" Whereupon the poet wrote his second epic.