Samuel Pepys mentions him in his diary on October 31st, 1661, as having "but come from Oxford" and meeting his father at Pepys' house. On the 25th of January, 1662, the Admiral discussed with Pepys a plan for sending his son to Cambridge or some private college. Pepys undertook to write Dr. Fairbrother and inquire into the merits of Hezekiah Burton at Magdalen, as an instructor for the difficult youth. It was impossible to fit him into any school under the dominion of the Church of England and in wrath his father forbade him the house. His mother interceded, with the result that he was sent to Europe for the grand tour, presumably with outward success, for on August 6, 1664, Mrs. Pepys informs Samuel that "Mr. Pen, Sir William's son, is come back from France and come to visit her. A most modish person, grown, she says, a fine gentleman."
After dinner on the 30th of the same month "comes Mr. Pen to visit me, and staid an hour talking with me. I perceive something of learning he has got, but a great deal, if not too much of the vanity of the French garb and affected manner of speech and gait. I fear all real profit he hath made of his travel will signify little."
The home coming soon stripped Penn of the "vanity of the French garb," and he became once more a problem. He tried the study of law, but could not interest himself in it. To keep him out of the way and repress his dangerous thoughts he was given the management in 1665, of an estate owned by the Admiral in Ireland, where he went and did as he pleased, falling in again with Thomas Loe and resuming his Quaker views. December 29th, 1667, Pepys records a call from Mrs. Turner "...and there, among other talk, she tells me that Mr. William Pen, who is lately come over from Ireland, is a Quaker again, or some very melancholy thing; that he cares for no company, nor comes into any; which is a pleasant thing, after his being abroad so long, and his father such a hypocritical rogue and at this time an Atheist."
This return he signalized by intense activity in pressing Quakerism upon the public, to the vexation of his father who was one of the notables of England, as Admiral both under Cromwell and the King. He had commanded the fleet of the Lord Protector which wrested the rich Island of Jamaica from Spain and as one of the three commissioners of the Navy, laid the foundation for that British fleet which has ever since played so large a part in the history of the world. He was the practical man of the commission, from whom James, Duke of York, afterwards, and very briefly King, took most of his advice. He reformed the higgledy-piggledy naval tactics of the time and taught the commanders to attack the enemy in line, the most important change in the sea annals of his country. Knighted in 1665 for service against the Dutch he failed of the peerage because of the public prejudice against his son, which deterred the King from giving him an honor as high as he deserved. As Clerk of the Acts, Pepys was much in contact with him socially and officially. The famous diary teems with references, many of them convivial, others most unkind. He was faithful to the commonwealth as long as it was faithful to itself. Perceiving that it could not hold together after the death of Cromwell he joined with George Monk in bringing about the restoration of the Stuarts.
Against this background of paternal distinction, the young reformer shone invidiously and brought his father great chagrin by his association with carpenters and weavers in their non-conformist agitations. He preached in poor halls and in the streets. The newspaper, not having arrived, he took to pamphleteering to spread his doctrines. This activity reached a crisis in 1669. Writing in his diary under date of February 12, 1669, Pepys says: "...Felling hath got me W. Pen's book against the Trinity. I got my wife to read it to me; and I find it so well writ as, I think, it is too good for him ever to have writ it, and it is a serious sort of book not fit for everybody to read."
The extended title of this work was "The Sandy Foundation Shaken—or those ...Doctrines of one God subsisting in three distinct and separate persons; the impossibility of God's pardoning persons by an imputative refuted from the authority of scripture testimonies and right reason," etc.
It was a drastic review of the doctrine of the Trinity and as the title implies, undertook to prove that the majestic edifice of the State Church was not founded upon a rock. It created much excitement and speedily landed its author in the Tower. Here he remained nine months, unrepentant and writing more pious sedition, to wit: "No Cross No Crown," and "Innocency With Her Open Face." These were further polemics against Episcopacy.
The King having no heart for persecution, and the Duke of York, who was a firm friend, contrived to have the prisoner released on the 4th of August and turned over to his father to be transported to some spot where he would be less troublesome. This plan was not seriously carried out. Indeed the Admiral's days were numbered. He died after a year's illness, on the 16th of September, 1670.
Penn's prominence and influence increased with the death of his father. It was plain that no ordinary mind directed his actions. Respect followed. He took much part in public matters and as umpire in a dispute between Fenwick and Byllinge, two Quakers, over some land rights in New Jersey, he developed an interest in the New World and planned to found in it a place of refuge for those persecuted in Old and New England for opinion's sake. This desire was readily carried out. By fortunate chance the Crown owed Admiral Penn's estate some $80,000. To pay this debt and be rid of an agitator, the shrewd King made an easy adjustment in 1681 by handing over to the heir a vast province between the Delaware and the Ohio, in return for an annual tribute of two beaver skins, to be paid for ninety-nine years.
Here the idealist created his elysium and came as close to making one as the curious animal he sought to benefit would permit. The King set forth in writing the Grant that it was due "the memory and merits of Sir William Penn in divers services, and particularly his conduct, courage and discretion under our dearest brother, James, Duke of York, in that signal battle and victory fought and obtained against the Dutch fleet commanded by the Heer Van Opdam, in 1665."