The commencement of open hostilities between the colonists and the British troops in May 1775, made Thompson's position still more critical. As a major in the militia of the province, he would probably have acted on the side of the patriots, obeying the orders of the Provincial Congress, which had superseded the old government; but the odium attached to his name was such, that his very zeal on the patriotic side would have been misrepresented. In order, therefore, to clear himself of all suspicion, and that he might thenceforth live on good terms with his countrymen, he demanded a trial before the Committee of Correspondence established at Woburn by authority of the new power. The trial was granted: he was put under arrest; and an advertisement was inserted in the newspapers for all who had charges to prefer against his patriotism to come forward. Besides the general allegation of his being a Tory, and a friend and correspondent of Governor Wentworth and General Gage, the only charge made against him on his trial was, that he had been instrumental in sending back to their colors two British deserters, having procured their pardon from General Gage during his residence in Boston. This, which ought properly to have been regarded as a mere act of mercy, was construed in a less favorable manner by Thompson's judges; and although, on the conclusion of his trial, the court declared that he had done nothing which could legally be considered as a crime, he was set at liberty without the satisfaction of a full and formal acquittal. Against this treatment he protested in the strongest manner, insisting that he should either be punished as guilty, or declared innocent; but his protests were unheeded.
With a view, apparently, to convince his countrymen of his patriotism by actual service, or possibly because he could enjoy more quiet in the army than the ill-will of his fellow-citizens would allow him in his own house, Thompson, as soon as his trial was over, joined a detachment of the troops of Congress stationed at Chelsea. In the hopes of obtaining a commission,' says his biographer, he paid great attention to tactics, and assisted at the drills of the yet undisciplined forces. He also took up the study of fortification, which he pursued with his usual ardor. Towards the close, however, Of the summer of 1775, his position had become irksome, and even dangerous. Suspicions, which it seemed impossible to allay, shut against him all access to military rank in the continental army. He now could not go from place to place within the lines of the army, without being pointed at as the famous Tory Thompson and though discipline sheltered him from actual violence, he was exposed to insults that a man of spirit could not brook, and which his position prevented. him from resenting. If thus treated within the army, he might infer what awaited him when he should emerge from the out-posts of the camp.' In these circumstances, he came to the desperate resolution of leaving his native country. I cannot any longer,' he writes to his father-in-law on the 14th of August 1775, bear the insults that are daily offered to me. I cannot bear to be looked upon and treated as the Achan of society. I have done nothing that can deserve this cruel usage. And notwithstanding I have the tenderest regard for my wife and family, and really believe I have an equal return of love and affection from them, though I feel the keenest distress at the thoughts of what Mrs. Thompson and my parents and friends will suffer on my account, and though I foresee and realize the distress, poverty, and wretchedness that must attend my pilgrimage in unknown lands, destitute of fortune, friends, and acquaintances, yet all these evils appear to me more tolerable than the treatment which I meet with at the hands of my ungrateful countrymen.'
Two months after writing the above, he carried his resolution into effect. Paying off his debts, and converting some of his property into cash, with the expressed intention of removing to some of the southern states, where he might live in greater security, he set out from Cambridge, the headquarters of the American army, on the 10th of October 1775, accompanied by his half-brother, Josiah Pierce, who took leave of him at the nearest post-town. From that hour,' says his biographer, until the close of the revolutionary struggle, his friends and relatives were without any positive tidings of his fate.' From accounts afterwards received, it appeared that he had reached Newport on the 11th of October, apparently undecided as to his future movements; that there finding a boat belonging to the British frigate Scarborough,he went on board that vessel, and was afterwards landed at Boston, which his friend General Gage, as commander of the British garrison, was at that time maintaining against the American forces. Here he remained under the protection of the British till the evacuation of the town in March 1776, when he again embarked on board the Scarborough, and set sail for England, the bearer of despatches from General Gage to Lord George Germain, the British secretary of state for colonial affairs. Thus had he fairly renounced all connexion with his native country, and gone to push his fortunes in the old world.