In 1686, when making a third missionary journey to Holland and Germany, Penn was charged by James with an informal mission to the prince of Orange to endeavour to gain his assent to the removal of religious tests. He gained no satisfaction either from the prince or from Burnet, who disliked him. On his return he went on a preaching mission through England. His position with James was undoubtedly a compromising one, and it is not strange that, wishing to tolerate Papists, he should, in the prevail ing temper of England, be once more accused of being a Jesuit. In 1687 James published the Declaration of Indulgence, and Penn probably drew up the address of thanks on the part of the Quakers. It fully reflects his views, which are further ably put in the pamphlet Good Advice to the Church of England, Roman Catholics and Protestant Dissenters, in which he showed the wis dom and duty of repealing the Test Acts and Penal Laws. At the Revolution he behaved with courage. He was one of the few friends of the king who remained in London, and, when twice summoned before the council, spoke boldly in his behalf. He admitted that James had asked him to come to him in France; but at the same time he asserted his perfect loyalty. During the absence of William in 1690 he was proclaimed by Mary as a dangerous person, but no evidence of treason was forthcoming. It was now that he lost by death two of his dearest friends, Robert Barclay and George Fox. It was at the funeral of the latter that, upon the information of the notorious informer William Fuller (167o-1717?), an attempt was made to arrest him, but he had just left the ground; the fact that no further steps were then taken shows how little the government believed in his guilt. He now lived in retirement in London, though his address was per fectly well known to his friends in the council. In 1691, again on Fuller's evidence, a proclamation was issued for the arrest of Penn and two others as being concerned in Preston's plot. In 1692 he began to write again, both on questions of Quaker discipline and in defence of the sect. Just Measures in an Epistle of Peace and Love, The New Athenians (in reply to the attacks of the Athenian Mercury), and A Key opening the Way to every Capacity are the principal publications of this year.
Meantime matters had been going badly in Pennsylvania. Penn had, in 1686, been obliged to make changes in the composition of the executive body, though in 1689 it reverted to the original constitution; the legislative bodies had quarrelled; and Penn could not gain his rents. The chief difficulty in Pennsylvania was the dispute between the province--i.e., the country given to Penn by the charter—and the "territories," or the lands granted to him by the duke of York by feoffment in August 1682, which were under the same government but had differing interests. The difficulties which Quaker principles placed in the way of arming the colony--a matter of grave importance in the existing European complica tions—fought most hardly against Penn's power. On Oct. 21, 1692 an order of council was issued depriving Penn of the gov ernorship of Pennsylvania and giving it to Colonel Benjamin Fletcher, the governor of New York. To this blow were added the illness of his wife and a fresh accusation of treasonable corre spondence with James. In his enforced retirement he wrote the most devotional and most charming of his works—the collection of maxims of conduct and religion entitled The Fruits of Solitude.
In December, thanks to the efforts of his friends at court, among whom were Buckingham, Somers, Rochester, and Henry Sidney, he received an intimation that no further steps would be taken against him. The accusation, however, had been public, and he insisted on the withdrawal being equally public. He was therefore heard in full council before the king, and honourably acquitted of all charges of treason. It was now that he wrote an Essay towards the Present and Future Peace of Europe, in which he puts forth the idea of a great court of arbitration, a principle which he had already carried out in Pennsylvania.
In 2694 (Feb. 23) his wife Gulielma died, leaving two sons, Springett and William, and a daughter Letitia, afterwards married to William Aubrey. Two other daughters, Mary and Hannah, died in infancy. He consoled himself by writing his Account of the Rise and Progress of the People called Quakers. The coldness and suspicion with which he had been regarded by his own denomi nation had now ceased, and he was once more regarded by the Quaker body as their leader. About the same time (Aug. 2o) he was restored to the governorship of Pennsylvania ; and he prom ised to supply money and men for the defence of the frontiers. In 1695 he went on another preaching mission in the west, and in March 1696 he formed a second marriage, with Hannah Callow hill, his son Springett dying five weeks later. In this year he wrote his work On Primitive Christianity, in which he argues that the faith and practice of the Friends were those of the early Church. In 1697 Penn removed to Bristol, and during the greater part of 1698 was preaching with great success against oppression in Ire land, whither he had gone to look after the property at Shannan garry.
In 1699 he was back in Pennsylvania where the success of Colonel Robert Quary, judge of the admiralty in Pennsylvania— who was in the interests of those who wished to make the province an imperial colony—and the high-handed action of the deputy Markham in opposition to the Crown, were causing great diffi culties. Penn carried with him particular instructions to put down piracy, which the objections of the Quakers to the use of force had rendered audacious and concerning which Quary had made strong representations to the home government, while Markham and the inhabitants apparently encouraged it. Penn and Quary, however, came at once to a satisfactory understanding on this matter, and the illegal traffic was vigorously and successfully attacked. In 1696 the Philadelphian Yearly Meeting had passed a resolution declaring slavery contrary to the first principles of the gospel. Penn, however, did not venture upon emancipation ; but he insisted on the instruction of negroes, permission for them to marry, repression of polygamy and adultery, and proposed regulations for their trial and punishment. The assembly, how ever, a very mixed body of all nations, now refused to accept any of these proposals except the last-named. His great success was with the Indians; by their treaty with him in 1700 they promised not to help any enemy of England, to traffic only with those approved by the governor, and to sell furs or skins to none but inhabitants of the province. At the same time he showed his capacity for legislation by the share he took with Lord Bellomont at New York in the consolidation of the laws in use in the various parts of America.