Under Elizabeth
A man so regarded could expect small consideration when the death of Mary (17 November 1558) placed Elizabeth on the throne. On her accession the new queen refused to allow him to kiss her hand; but he sat and voted in the parliament and convocation of 1559. From 24 June 1559, the Mass was forbidden as well as all other services not in the Book of Common Prayer, but long before that date the Mass ceased in most London churches, though Bonner took care that in his cathedral at least it should still be celebrated. In May he refused to take the oath of supremacy, acquiring like his colleagues consistency with old age. According to an envoy from the Court of Mantua, Bonner resisted orders to remove the service of the Mass by saying, "I possess three things soul, body, and property. Of the two latter, you can dispose at your pleasure, but as to the soul, God alone can command me."
The Council ordered him to resign the bishopric, which he refused to do, adding that he preferred death. He was sent again to the Marshalsea on 20 April 1560. During the next two years representatives of the Protestant party frequently clamored for the execution of Bonner and the other imprisoned bishops. When the Parliament of 1563 met, a new Act was passed by which the first refusal of the oath of royal supremacy was praemunire, the second, high treason. The bishops had refused the oath once, so that by this Act, which became law on 10 April 1563, their next refusal of the oath might be followed by their death.
Thanks to the intervention of the Spanish ambassador, action against the bishops was delayed; but a year later, on 29 April 1564, Bonner was indicted on a charge of praemunire on refusing the oath when tendered him by his diocesan, Bishop Horne of Winchester. He challenged the legality of Horne's consecration, and a special act of parliament was passed to meet the point, while the charge against Bonner was withdrawn. Four times a year for three years he was forced to appear in the courts at Westminster only to be further remanded. The last of these appearances took place in the Michaelmas term of 1568, so that the last year of the bishop's life was spent in prison. His demeanor during his long imprisonment was remarkable for his cheerfulness, and even Jewel describes him in a letter as "a most courteous man and gentlemanly both in his manners and appearance" (Zurich Letters, I, 34).
Bonner never tired of trying to convert others to Catholicism, and never repented of his crimes to Protestants. Bishop Jewel in a letter to Peter Martyr related this event, "Being confined to the tower of London upon accession of Queen Elizabeth, the highest punishement inflicted, he went to visit some of the criminals kept in that prison, and wishing to encourage them, called them his friends and neighbors." Upon this, one of them is said to have answered, "Go beast, into hell, and find your friends there, for we are none of them. I killed but one man upon a provocation, and do truly repent of it; but you have killed many persons of all sorts, without any provocation from them, and are hardened in your impenitence." He died in the Marshalsea on 5 September 1569, and was buried in St George's, Southwark, secretly at midnight to avoid the risk of a hostile demonstration. According to Catholic sources, the coffin was soon quietly removed to Copford, near Colchester, where it was buried under the north side of the altar.
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