London, in company with Archbishop Alexander Burnet [q. v.] of Glasgow, to represent to the king and the English bishops the state of ecclesiastical affairs in Scotland; and on his return shortly afterwards was created D.D. at St. Andrews by the instrumentality of Archbishop Sharp. Having now returned to England, promotions came to him in quick succession. After taking the degree of D.D. at Oxford on 17 Dec. 1679, he was made prebendary of Worcester in June 1680, vicar of All Hallows Barking in August 1680, chaplain to the king in December 1681, and in August 1683, upon the recommendation of the ecclesiastical commissioners to the king, dean of Worcester. Shortly after his going to All Hallows he was indicted on a ridiculous charge of idolatry in bowing to a wooden image of St. Michael over the communion-table. The indictment was quashed on the ground that the charge was not one to be brought before a civil court. The image was then broken in pieces by one of the churchwardens and burned in the vestry. Of this case Hickes printed a narrative, ‘Of an Apparition of an Archangel at the Old Baily,’ in a single sheet. After his promotion to the deanery of Worcester, lord-keeper North desired him, by the king's command, to study the patent rolls, with a view to further promotion, the king saying that, through ignorance of these, the bishops since the Reformation had been the worst members of parliament in the House of Lords, and of the least influence. The dean had reached, in consequence, a third volume of transcripts lent him by the lord keeper when the king died, and he then gave up the task. He had previously, in 1684, declined the bishopric of Bristol, with which he might have held his deanery in commendam. He resigned the vicarage of All Hallows in May 1686, being appointed instead to the rectory of Alvechurch, not very far from Worcester. At Worcester he began his study of the northern languages, and after one year's indefatigable work, compiled his ‘Anglo-Saxon and Mœso-Gothic Grammar,’ which was printed at Oxford in 1689. When in 1687 Bishop Thomas of Worcester was ill, it was feared that James II might try to fill a vacancy with some adherent to his projects, but Hickes assured the prebendaries that he would first pray the king to recall any congé d'élire issued for such a person, and then, if necessary, endure any penalty rather than summon the chapter to elect. He was strongly opposed to the king's declaration of indulgence, and in a letter of 5 Nov. 1687 to Edmund Bohun [q. v.] (signed ‘Gregory Hopt.’) expresses a hope that Bohun will preserve for future ages a register of the names of those confessors, a cloud of witnesses, who ‘were removed from honourable and beneficial places merely upon the score of religion when their loyalty was acknowledged’ (original manuscript letters in the possession of Mr. C. H. Firth of Balliol College, Oxford). A letter on the same subject to Dean Comber, dated 9 June 1688, after the order for publication of the declaration in the churches, is printed in the ‘Orthodox Churchman's Magazine,’ 1802, ii. 321–2. But during Monmouth's rebellion his loyalty was unshaken. His brother John [q. v.] engaged in it, and was executed on 6 Oct. 1685. The dean exerted himself in vain for his deliverance, offering 100l. to Lord Shannon to procure a pardon for him by the king's personal favour.
The Sunday after the landing of the Prince of Orange the dean preached in his cathedral a sermon upon the example of primitive Christians in submission to persecuting princes, and suffered, in consequence, some trouble at the hands of a considerable force which had secured the city of Worcester for the prince. Refusing the oath of allegiance, he was suspended on 1 Aug. 1689; and, after six months' interval, was deprived on 1 Feb. following. He remained, however, unmolested until the beginning of May, and then, upon hearing of the appointment of his successor in the deanery, he affixed to the entrance-gate of the choir of the cathedral a claim of right against all intruders. This was set up before morning prayer on 2 May, and in the middle of evening service was removed by an officer. In the drawing up of this document, which is printed in the appendix to Lee's ‘Life of Kettlewell,’ p. v, he was assisted by the advice of Mr. North [query Roger North?], whose modifications are given in a draft which is preserved in the Bodleian Library (Engl. Hist. MS. b 2, fol. 110). Messengers were then sent by the Earl of Nottingham, secretary of state, for his arrest, but Hickes had meanwhile secretly withdrawn to London, where, and in the neighbourhood, he remained more or less in concealment, until, in 1699, Lord-chancellor Somers caused a nolle prosequi to be entered to all proceedings against him. During some earlier part of this period he was harboured by White Kennett, then rector of Ambrosden, Oxfordshire, and disguised himself in lay attire, sometimes assuming that of a military officer. He lived also for a time at Westwood in Worcestershire, under the roof of Lady Pakington, to whom he assigns, in his preface to his ‘Thesaurus,’ the authorship of the ‘Whole Duty of Man.’