Elizabeth's first Parliament gave over to her all the religious houses revived by her sister, and she decided to once more make Westminster a Cathedral church, though without a bishopric. Possibly if Fakenham had been a more time-serving man, he might have managed to stay on under the new regime as Dean, but he was uncompromisingly true to his principles; he refused to acknowledge any one but the Pope as head of the Church, and in the House of Lords he made a strong speech against the English Prayer-Book. His reign at Westminster had been a short one, but he had not failed in his duty towards the precious trust committed to his care. The Confessor's Chapel, shrine of the English saint, was still the greatest treasure of the Abbey, and to this he had caused the body of the king, hidden, you will remember, by the monks at the first threat of dissolution, to be carried back "with the most goodly singing and chanting ever heard," after he had repaired the shrine itself to the best of his ability, assisted by Queen Mary, who had sent him some jewels. Moreover, in Parliament he successfully defended the right of sanctuary, so that this remained for some time longer at least an Abbey privilege, and altogether it is pleasant to remember this last Abbot as one who was true to the light as he saw it, a kindly, moderate, honest man, a firm friend, a fair enemy, a fine solitary figure standing out among his fellows. It is said that when in 1560 the bill was passed in Parliament which decided the fate of Westminster and the other remaining monasteries, a messenger who came to bring the news to Abbot Fakenham found him busy planting young elms in the Dean's yard.
"Cease thy labours, my lord Abbot," he said. "This planting of trees will avail thee nothing now."
But the old Abbot was not so mean-spirited.
"I verily believe," he made answer, "that so long as this church endureth, it shall be kept for a seat of learning."
And he went on contentedly with his work.
He lived for twenty-five years after he left the Abbey, under a certain amount of restraints, and great efforts were made to induce him to change his faith. But he never wavered, and so far as possible withdrew from all controversy, spending his time and his substance among the poor. "Like an axil tree, he stood firm and fixed in his own judgments," says Fuller, "while the times, like the wheels, turned backwards and forwards round him."