About a year after his commitment to the tower, by the importunity of Queen Ann, he was arraign'd at the King's Bench Bar, for obstinately refusing, the oath of supremacy, and wilfully and obstinately opposing the King's second marriage. He went to the court leaning on his staff, because he had been much weakened by his imprisonment; his judges were, Audley, Lord Chancellor; Fitz James, Chief Justice; Sir John Baldwin, Sir Richard Leister, Sir John Port, Sir John Spelman, Sir Walter Luke, Sir Anthony Fitzherbert: The King's attorney opened against him with a very opprobrious libel; the chief evidence were Mr. secretary Cromwell, to whom he had uttered some disrespectful expressions of the King's authority, the duke of Suffolk and earl of Wiltshire: He replied to the accusation with great composure and strength of argument; and when one Mr. Rich swore against him, he boldly asserted that Rich was perjured, and wished he might never see God's Countenance in mercy, if what he asserted was not true; besides that, Rich added to perjury, the baseness of betraying private conversation. But notwithstanding his defence, the jury, who were composed of creatures of the court, brought in their verdict, guilty; and he had sentence of death pronounced against him, which he heard without emotion. He then made a long speech addressed to the Chancellor, and observed to Mr. Rich, that he was more sorry for his perjury, than for the sentence that had just been pronounced against him: Rich had been sent by the secretary to take away all Sir Thomas's books and papers, during which time some conversation passed, which Rich misrepresented in order to advance himself in the King's favour. He was ordered again to the Tower till the King's pleasure should be known. When he landed at Tower Wharf, his favourite daughter Margaret, who had not seen him since his confinement, came there to take her last adieu, and forgetting the bashfulness and delicacy of her sex, press'd thro' the multitude, threw her arms about her father's neck and often embraced him; they had but little conversation, and their parting was so moving, that all the spectators dissolved in tears, and applauded the affection and tenderness of the lady which could enable her to take her farewel under so many disadvantages.