In 1783 Thomas Muir became involved in a conflict with the Principal of Glasgow University when he organised a petition against the suspension of Professor John Anderson. As a result of his campaign to have Anderson reinstated, Muir was expelled from the university. With the help of Millar, Muir finished his studies at Edinburgh University and entered the Faculty of Advocates in 1787.

Muir soon developed a reputation as a lawyer who was willing to appear in court on behalf of poor clients who could not afford to pay a fee. He also became a fierce critic of a legal system that he believed was biased in favour of the rich.

The French Revolution in 1789 inspired supporters of parliamentary reform all over Britain. Young members of the Whigs in London formed the Society of the Friends of the People in April 1792. Groups were soon formed in other parts of Britain and on 26th July 1792, Thomas Muir and William Skirving established the Scottish Association of the Friends of the People. Branches were formed in Perth, Dundee, Glasgow and Edinburgh. By November there were eighty-seven branches of the Society of Friends in Britain. Thomas Muir now began to organize a General Convention of these Societies in order to develop a strategy for the achievement of parliamentary reform.

The British government became concerned about Thomas Muir and a spy was recruited to gather information about his political activities. After the spy had gathered what was considered enough evidence, Thomas Muir was arrested on 2nd January, 1793, and charged with sedition. After being interrogated for several hours he was released on bail.

Muir now travelled to London where he had talks with the leaders of the Friends of the People. The leaders of the movement were concerned about the violence taking place in France. Muir agreed to go to France and join Tom Paine in his attempts to persuade the leaders of the revolution to abandon the plan to execute Louis XVI.

Muir was unsuccessful and after having talks with the Girondist leaders, he returned to Scotland on 23rd August. The following day Muir was arrested and after being imprisoned in Edinburgh was tried for sedition before Lord Braxfield and a hand-picked jury of anti-reformers. Muir was found guilty and sentenced to fourteen years' transportation. Afraid that Scottish reformers would attempt to rescue Muir, he was quickly removed to London. Soon afterwards he was joined by other leaders of the movement, Fyshe Palmer, William Skriving and Maurice Margarot.

Radicals in the House of Commons immediately began a campaign to save the men now being described as the Scottish Martyrs. On 24th February, 1793, Richard Sheridan presented a petition to Parliament that described the men's treatment as "illegal, unjust, oppressive and unconstitutional". Charles Fox pointed out in the debate that followed that Palmer had done "no more than what had done by William Pitt (now Prime Minister of Britain) and the Duke of Richmond" when they campaigned for parliamentary reform.

Attempts to stop the men being transported failed and on 2nd May 1794, The Surprise left Portsmouth and began its 13,000 mile journey to Botany Bay. The men arrived on 25th October to join the Colony of 1,908 convicts (1362 male, 546 female). As a political prisoner, Muir was given more freedom than most convicts and he was allowed to buy a small farm close to Sydney Cove.

After two years at Port Jackson, New South Wales, Thomas Muir escaped with the help of Francis Peron, the chief mate of the American ship, the Otter of Boston. Muir reached Vancouver Island but after being offered help by a Spanish captain, he was arrested and taken on board the Ninfa. While on the way to Cadiz the Ninfa was attacked by the British warship Irresistible. During the battle Thomas Muir was hit by a glancing blow from a cannonball which smashed his left cheekbone and seriously injured both his eyes.

For several days Muir's condition was so bad he was expected to die. When the French government heard about what had happened to Muir they tried to persuade the Spanish authorities to release him. The Spanish eventually agreed and Muir arrived in Bordeaux in November 1797.

Muir joined up with Tom Paine in Paris where they continued the fight for parliamentary reform in Britain. However, Muir had never fully recovered from the wound he received on the Ninfa and his health began to deteriorate at the end of 1798. Thomas Muir was taken to Chantilly where he died on 26th January, 1799.

In 1845 Thomas Hume, the Radical MP organised the building of a 90 feet high monument in Waterloo Place, Edinburgh. It contained the following inscription: "To the memory of Thomas Muir, Thomas Fyshe Palmer, William Skirving, Maurice Margarot and Joseph Gerrald. Erected by the Friends of Parliamentary Reform in England and Scotland." On the other side of the obelisk, based on the model of Cleopatra's Needle in London, is a quotation from a speech made by Muir on 30th August, 1793: "I have devoted myself to the cause of the people. It is a good cause - it shall ultimately prevail - it shall finally triumph."