In 1770, however, he resumed his mercantile avocations in the capacity of a clerk at a dry goods store at Boston, kept by a Mr. Capen, and was thus engaged during the famous riots which took place in that town, on the attempt to land a cargo of tea from a British vessel, contrary to a resolution of the colonists against admitting British goods. These disturbances caused Mr. Capen's business to decline as Mr. Appleby's had formerly done, and Thompson was again obliged to return to Woburn. He now seriously turned his attention to the acquisition of scientific knowledge, and in company with his friend Baldwin attended a course of lectures on experimental philosophy delivered at Harvard College, instituting at the same time many experiments of his own, some of which proved the germs of valuable conclusions published in after life. In particular may be mentioned a course of experiments which he began in order to ascertain and measure the projectile force of gunpowder.

Thompson, though still only in his seventeenth year, had now acquired a certain amount of reputation; he was also endowed with much natural grace and many personal advantages, which subsequently proved the means of gaining him access to the first circles in Europe.

Towards the close of the year 1770 he was invited by Colonel Timothy Walker, one of the most important residents in the village of Rumford, now Concord, in New Hampshire, to take charge of an Academy in that place. Two years later, at the age of twenty, he married Mrs. Rolfe, a colonel's widow possessed of a considerable fortune. After his marriage Thompson took his place as one of the wealthiest inhabitants of the district in which he resided, mixing with the best society the colony afforded. Among others he made the acquaintance of the governor John Wentworth, who, wishing to attach to the British party so influential a colonist, gave Thompson the commission of major in a regiment of the New Hampshire Militia, in which a vacancy had occurred. This act of attention, while gratifying to Thompson, procured him much ill-will from the officers already in the service, and over whose head he had been promoted.

From this period he began to be unpopular in his native country. He was represented as a friend of Great Britain, and an enemy to the interests of the colonies. The public hatred of him at length rose to such a height, that he only escaped by flight from the ignominy of being tarred and feathered in the open streets. Leaving his wife and an infant daughter, Thomas first took refuge in his native town of Woburn, and then proceeded to Charlestown where he remained for several months. From Charlestown he went to Boston, at which place he was well received by General Gage and the officers of the British army at that time in garrison at Boston. Returning in the spring of 1775 to Woburn, he again ran the risk of being tarred and feathered, but was saved by the interference of his friend Baldwin.

The commencement of open hostilities between the Colonists and the British troops in May, 1775, made Thompson's position still more critical, and finding that he could not overcome the prejudice felt against him, he came to the desperate resolution of quitting his native country, and leaving his wife and child. To effect this he first escaped to Boston, where he remained, with his friend General Gage, until the evacuation of the town by the British troops, when he embarked on board the Scarborough, and set sail for England, with despatches from General Gage to Lord George Germain, the British Secretary of State for Colonial Affairs.

Although Thompson arrived in England the bearer of gloomy tidings, and sustaining the equivocal character of a deserter from the American cause, he soon showed that he was a man capable of commanding his fortune anywhere. The capacity in which he had come over introduced him to various public men who were both struck by his abilities and charmed by his manners. But a short time elapsed after his arrival before he was offered a post in the Colonial Office, and four years after, in 1780, was raised by his patron Lord Germain to the post of under secretary for the colonies, an instance of rapid promotion which, considering the circumstances in which the subject of it stood, is almost unexampled.

The income and consequence which Thompson derived from this office gave him admission to the highest metropolitan circles, and he had thus opportunities not only of becoming known, but also of exercising his inventive mind in many pursuits not immediately connected with his official duties. Fertility of resources, and a disposition to propose improvements in all departments, appear to have been his most striking characteristics, and it was probably this ready genius for practical reform in everything which came under his notice, that recommended him so much to public men. While engaged generally in a variety of matters, Thompson was at the same time following out certain specific lines of scientific investigation. His experiments on the heat caused by friction, deduced from the boring of cannon, are among the best we possess.

In 1777 he made some curious and interesting experiments on the strength of solid bodies, which were, however, never published. In 1778 he employed himself in further experiments on the strength of gunpowder and the velocity of military projectiles; and these were followed up by a cruise of some months in the Channel fleet, where he proposed to repeat his experiments on a larger scale. He communicated the result of his researches on this subject, in several papers, to the 'Philosophical Transactions' of the Royal Society, of which he became a member in the last-mentioned year.

On the retirement of Lord George Germain from office, Thompson was sent out to New York in the year 1781, with the royal commission of major, afterwards changed to that of lieutenant-colonel, charged with the task of organizing an efficient regiment of dragoons out of the broken and disjointed native cavalry regiments which had been fighting on the royalist side. This regiment was, however, of no avail; peace was concluded between Great Britain and the United States, and Colonel Thompson on his return to England obtained leave of absence to travel on the Continent. In crossing from England to France, it happened that he had as a fellow-traveller the celebrated historian Gibbon, who, in some subsequent correspondence, spoke of him as "the soldier, philosopher, statesman—Thompson."

While on his way to Vienna, Thompson attended a review of the garrison of Strasbourg, and, attracting general attention by his superb English horse and uniform of colonel of dragoons, became introduced to the notice of Prince Maximilian, nephew and presumptive heir of the Elector of Bavaria. This prince was agreeably impressed by the manners and address of Thompson, and furnished him with letters of introduction to his uncle, the Bavarian Elector. When Thompson arrived at Munich (so great seems to have been his power of conciliating favour), he was offered, on his first interview with the elector, an important situation at court, if he would take up his residence there. After a little delay, Thompson accepted this offer, conditional upon receiving permission from his Britannic Majesty. Proceeding to London to obtain the required consent, he was very favourably received by George III., who conferred on him the honour of knighthood, and allowed him to retain his title of lieutenant-colonel, together with the half-pay attached to it.