Aylesbury again in 1656 for the Second Protectorate Parliament In 1659, he was elected MP for Wycombe again in the Third Protectorate Parliament and then sat for Aylesbury again in the restored Rump Parliament. Like all of the other 59 men who signed the death warrant for Charles I he was in grave danger when Charles II of England was restored to the throne. He fled to Flanders, but surrendered at Brussels. He was put on trial, found guilty and hanged, drawn and quartered on 17 October 1660 for the crime of regicide. Thomas Scot was brought to trial on 12 October 1660 (in the opinion of Edmund Ludlow the outcome was a foregone conclusion). He was charged with sitting in the High Court of Justice at the trial of King Charles I and with signing one warrant for summoning that court, and another for the execution. He was further accused of wanting "Here lies Thomas Scot, who adjudged the late King to die" on his gravestone. Many witnesses were produced to prove these things; and among them William Lenthal, Speaker in the Long Parliament, who, when the King entered the House of Commons in 1641, and had demanded of him the Five Members, had answered "that he had neither ears to hear, eyes to see, or mouth to speak except what the House gave", now appear for the prosecution; affirming in Court, that Scot, had justified proceeding against the Charles in the House of Commons. In his defence, Scot said that whatever had been spoken in the House ought not to be given in evidence against him, not falling under the cognisance of any inferior court, as all men knew: that for what he had done in relation to the King, he had the authority of the Long Parliament for his justification and that this Court had no right to declare whether that authority were a Parliament or not; and being demanded to produce one instance to show that the House of Commons was ever possessed of such an authority, he assured them he could produce many. But having begun with the Saxon times, he was interrupted by the Court, and told that the things of those ages were obscure. Scot then moved on to a second defence that: He was interrupted by the Court in mid sentence; and John Finch said (according to Ludlow with passion): Scot replied: