Nothing is known for certain about Scot's early life until 1626, when he made an advantageous marriage to Alice Allinson of Chesterford in Essex. In 1644, he was a member of the county committee for Buckinghamshire; in 1645 he was elected recruiter MP for Aylesbury. Scot emerged as a zealous Independent and supporter of the King's trial, serving as a member of the High Court of Justice and signing the King's death warrant. He became prominent in the government of the Commonwealth as a leading member of the Council of State, and was sometimes referred to by the title Secretary of State.
In July 1649, the Council of State commissioned Scot to manage the spying and intelligence network essential for the security of the Commonwealth, both at home and abroad. He employed agents in foreign courts and among Royalist exiles, and came to have an important influence on English foreign and domestic policy. The network established by Scot was later directed by John Thurloe.
As a strong supporter of the republican Commonwealth, Scot vehemently opposed Cromwell's assumption of the office of Lord Protector. He was elected to the First Protectorate Parliament in 1654 as MP for Wycombe but was among the Members excluded from Parliament for refusing to sign the Recognition of the Protectorate insisted upon by Cromwell. Two years later, he was elected MP for Aylesbury in the Second Protectorate Parliament and once again was one of 100 republicans excluded from the first session of Parliament. The excluded Members were admitted to the second session, which opened in January 1658, and Scot became one of the leading critics of the new second chamber, or Upper House, established by Cromwell under the terms of the Humble Petition and Advice.
After Cromwell's death in September 1658, Scot was elected to the Third Protectorate Parliament called by Richard Cromwell in January 1659, during which he was among the opposition MPs who worked for the overthrow of the Protectorate. After Richard's resignation and the re-establishment of the Purged Parliament, Scot once again became a prominent member of the Council of State and resumed his former role as director of intelligence. When Major-General Lambert forcibly dissolved Parliament and the Council of State in October 1659, Scot was elected President of the nine members of the Council who refused to accept the dissolution and continued to meet in secret in defiance of the military junta. Scot and his associates appealed to General Monck and his army in Scotland to uphold the Commonwealth. With Monck's support, Parliament was duly reinstated in December 1659 and Scot was appointed Secretary of State in January 1660. However, Monck went further than the republicans expected by recalling the MPs excluded at Pride's Purge in 1648. The restored Long Parliament voted for new elections and set in motion the train of events that led to the Restoration of the monarchy in May 1660.
Denounced as a regicide, Scot fled to Brussels in April 1660. He was persuaded to give himself up in the hope of obtaining a pardon but he was sentenced to death at his trial in October 1660. Scot was hanged, drawn and quartered at Charing Cross on 17 October 1660. He conducted himself bravely at his execution and died unrepentant "in a cause not to be repented of."
References:
C. H. Firth, revised by Sean Kelsey, Thomas Scot, Oxford DNB, 2004
Godfrey Davies, The Restoration of Charles II, 1658-60, 1955