I can’t confirm that Gardiner actually called the Pope his enemy, but I haven't been able to look at his anti-Papal (actually, pro-royal supremacy) tracts or his book De Vera Obedientia in full, only excerpts. Edmund Bonner wrote a very vituperative preface to the second edition of Gardiner's book, which may have contained a reference to the Pope as "the enemy." Looking through the standard sources on Gardiner, Muller’s Stephen Gardiner and the Tudor Reaction and Redworth’s In Defence of the Church Catholic, I did not find any account of Gardiner referring to the Pope specifically with this term.
A clue to Gardiner’s spiritual beliefs and attitude toward the Pope is suggested by the Redworth’s title, In Defence of the Church Catholic. By training a brilliant lawyer who admitted to the king in the early 1530s that he knew “little of divinity,” Gardiner championed an English Catholic church governed by the episcopate, preserving the traditions handed down over the centuries. Redworth claims that Gardiner’s “legal training … profoundly affected his religious views. It consolidated his deep-rooted distrust of change and alteration. The student of Roman law had drummed into his head the notion of the authority of the law-giver, namely the emperor, whose rights and prerogatives had in many ways simply been assumed by the pope of Rome … Interestingly, it has long been known that those English bishops who received a university training in law were more likely to accept the Royal Supremacy over the English Church, as it was the simple substitution of one legitimate authority for another.”He embraced the royal supremacy after Henry demonstrated his severe displeasure with Gardiner’s attempt to preserve the Church’s independence (he wrote Convocation’s response to the Supplication against the Ordinaries. Instinctively a conservative, Gardiner appears to have believed that his conception of the Church would be best safeguarded by a strong protector. As Wolsey’s agent in Italy, ruthlessly bullying the Pope into granting the commission for the Blackfriars trial, Gardiner had not been impressed by the helpless Pope living exiled in the squalor of Orvieto. In Redworth’s words, “The see of Rome had squandered her prestige and independence in the search for temporal glory and was in no position to defend the truths of Catholicism.” Hence his surrender to Henry and the anti-papal works he wrote in the 1530s.
Gardiner’s doctrinal views were probably not as hardline as those embodied in the Six Articles he was accused of authoring in the late 1520s. He fudged on the Real Presence during his later career, calling it simply “the presence” and claiming not to know how it was accomplished, and obeyed the Edwardian council in refraining from preaching on it. But in 1551, brought to trial, he made a ringing affirmation of the Real Presence and “the Roman ‘doctrine of transubstantiation.’ Perhaps this was the moment when Stephen Gardiner felt again the need for papal Catholicism.” (Redworth)In the great sermon he delivered on St. Peter’s Day in 1548 he described ceremonies as “indifferent things” (not essential to doctrine and hence a matter for the government to decide.) Redworth: “He then denied there was any scriptural basis for papal authority.” Gardiner also attacked the religious orders, pilgrimages, and images, and declared the essential components of religion to be preaching and baptism.Although he made his career out of the Reformation, he never liked hard-line Protestant doctrine because of its social implications. Muller’s book discusses Gardiner’s attitude towards radical Robert Barnes: “His principal dogma, that of justification by faith only, with its emphasis on Christian liberty and its discount of good works, appeared to Gardiner to tend directly to licence and evil works … No less destructive of civil and social life did Gardiner find the teaching concerning predestination and election which was bound up with Barnes’ doctrine that man of his own free choice could do no good thing … Mischievous as these doctrines appeared, Barnes’ teaching that civil laws were not necessarily binding on the conscience appeared more mischievous still.”
So how did he end up Mary’s Chancellor, organizing the return to Rome and welcoming Cardinal Reginald Pole to England? The novice queen recognized she needed someone of his stature, authority, experience and ability to support her as England’s first female ruler (pace Jane Grey and Matilda) in a disputed succession, amid religious turmoil. Gardiner was widely agreed to be the most brilliant lawyer in Henry’s toolkit; his religious views were acceptable to the queen (she would not select an evangelical as Chancellor, however able) and his private life was free from scandal. Choosing him sent an immediate signal to radical Protestants that there would be at the very least a return to the Henrician settlement and, in view of his rousing defense of the Real Presence, energized Catholics with hope of a reunion with Rome. He understood the business and process of government, was familiar with all the surviving personalities of Henry’s and Edward’s reigns, had considerable diplomatic experience as the king’s envoy in France and the Low Countries, and frankly knew where the bodies were buried. As a bonus, the French hated him, which could only be a recommendation to the pro-Imperial queen. And Gardiner's view? Muller concludes that "While far from averse to the reform of ecclesiastical abuses and the abolition of superstitious practices, Gardiner’s aim in things ecclesiastical was to keep the English Church Catholic in doctrine and practice and to preserve in both Church and Realm the preserve and prerogative of the episcopate. In this his motive was as truly national as it was ecclesiastical, for it was his conviction that only by preserving at once the Catholicity and the power of the Church could the Realm be saved from such civil strife as was making a shambles of Germany ... He can hardly be blamed for concluding that the religious innovations of Somerset and Northumberland had some connection with the arrant misgovernment, the extreme economic distress, and the final treason of the reign … There was nothing left for one of his training and temperament but to look to the Papacy as the one hope for both Church and Realm.”
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