In the funeral obsequies at Henry's interment Gardiner assumed the leading part, and was the chief celebrant at the mass. It appeared, however, that in the royal will—a document to which considerable suspicion attaches—he was unnamed. According to Fuller (Church Hist. bk. v. 254) Henry had made the omission purposely, and when his attention was drawn to it replied that ‘he knew Gardiner's temper well enough, and though he could govern him, yet none of them would be able to do it.’ On Edward's accession Gardiner was excluded from the council of state, and also removed from the chancellorship of the university of Cambridge.
To the innovations in matters of religious doctrine and practice which followed on the assumption of the supreme authority by the council, Gardiner offered a consistent and uncompromising resistance; and on 25 Sept. 1547 was committed to the Fleet on the charge of having ‘spoken to others impertinent things of the King's Majesty's Visitations, and refused to set forth and receive the Injunctions and Homilies’ (MS. Privy Council Book, p. 229). After a fortnight Cranmer sent for him and endeavoured to prevail upon him to accept the homilies, hinting at the same time that if conformable in this respect he might hope again to become a privy councillor. Gardiner, however, continued contumacious. He was notwithstanding treated with considerable leniency, and after the proclamation of the general amnesty (24 Dec.) was permitted to return to his diocese. Amid the numerous changes which Somerset was now seeking to carry into effect he was especially anxious to have the formal concurrence of the episcopal order, and especially of Gardiner. The latter, although he alleged ill-health, was accordingly summoned to London (May 1548), and called upon to satisfy the council with respect to his views by the delivery of a public sermon. With this command he complied in a sermon preached at Paul's Cross (29 June), in which, however, while professing his readiness to yield a general obedience to the new legislation, he stoutly maintained the doctrine of the real presence, and omitted altogether to recognise the authority of the council. He was thereupon sent to the Tower, where he was detained in close confinement for a year.
On the fall of Somerset his hopes of regaining his freedom were destined to cruel disappointment. His repeated protests to the council against the illegality of his confinement were disregarded, and a petition to parliament which he drew up was not suffered to reach its destination. But at length the lords intimated a willingness to consider his case. Commissioners were sent to interrogate him and to procure his signature to certain articles. As, however, these involved not only a recognition of the ecclesiastical supremacy of the council, but also a repudiation of the six articles, together with an admission of the justice of his own punishment, Gardiner refused to make so humiliating a submission. The council accordingly proceeded to sequestrate the fruits of his bishopric, while the conditions of his confinement were made still more rigorous. Burnet himself admits that Gardiner's treatment was now ‘much censured, as being contrary to the liberties of Englishmen and the forms of all legal proceedings.’ In December 1551 he was brought to Lambeth for formal trial by a court presided over by Cranmer. Among the charges brought against him was that of having armed his household when resident in his diocese, a measure which he fully justified by pointing out that it was a precaution warranted by the disordered state of the neighbourhood at that time. From the other charges he vindicated himself by a general oath of compurgation, and it is deserving of special note that he expressly attributed the omission of his name from the late king's will to the machinations of his enemies. On 18 April 1552, however, he was deprived of his bishopric and sent back to the Tower, where he remained until the following reign. His successor in his see was Poynet, with Bale for his secretary. He had already (about February 1549) been deprived of the mastership of Trinity Hall.
On Mary's accession he was among the prisoners who knelt before her on her visit to the Tower, and was at once set at liberty. On 23 Aug. 1553 he was made lord high chancellor of the realm, and in this capacity placed the crown on her head at her coronation (1 Oct.), and presided at the opening of parliament (5 Oct.) In the same year he was re-elected to the chancellorship at Cambridge and to the mastership of Trinity Hall. For the severities put in force against the protestants in the earlier part of Mary's reign, Gardiner, in conjunction with Bonner, has generally been represented as mainly responsible. But it is certain that he sought (whatever may have been his motives) to save Cranmer's life, and also that of one with far less claims to mercy, Northumberland. Thomas Smith, who had been secretary to King Edward, was shielded by him from persecution, and even allowed 100l. per annum for his support; while Roger Ascham was continued in office as secretary and his salary increased. Gardiner also honourably interposed to prevent the committal of Peter Martyr to prison, and furnished him with the funds necessary to
