While at Woburn, his wife and child joined him, and stayed there for some months. At length he was arrested and confined in the town upon suspicion of being inimical to the interests of his country. When he was brought before the Committee of Inquiry, there was no evidence brought against him. Major Thompson then petitioned to be heard before the Committee of the Provincial Congress at Washington. This petition he entrusted to his friend Colonel Baldwin to present. The petition was referred by the committee to Congress, by whom it was deferred for the sake of more pressing business. At length he secured a hearing in his native town, but the result was indecisive, and he did not obtain the public acquittal that he desired, though the Committee of Correspondence found that the "said Thompson" had not "in any one instance shown a disposition unfriendly to American liberty; but that his general behaviour has evinced the direct contrary; and as he has now given us the strongest assurances of his good intentions, we recommend him to the friendship, confidence, and protection of all good people in this and the neighbouring provinces." This decision, however, does not appear to have been made public; and Thompson, on his release, retired to Charlestown, near Boston. When the buildings of Harvard College were converted into barracks, Major Thompson assisted in the transfer of the books to Concord. It is said that, after the battle of Charlestown, Thompson was introduced to General Washington, and would probably have received a commission under him but for the opposition of some of the New Hampshire officers. He afterwards took refuge in Boston, and it does not appear that he ever again saw his wife or her father. His daughter he did not see again till 1796, when she was twenty-two years of age. On March 24, 1776, General Washington obliged the British troops to evacuate Boston; Thompson was the first official bearer of this intelligence to London. Of course, his property at Concord was confiscated to the commonwealth of Massachusetts, and he himself was proscribed in the Alienation Act of New Hampshire, in 1778. When Thompson reached London with the intelligence of the evacuation of Boston, Lord George Germaine, the Secretary for War, saw that he could afford much information which would be of value to the Government. An appointment was soon found for him in the Colonial Office, and afterwards he was made Secretary of the Province of Georgia, in which latter capacity, however, he had no duties to fulfil. Throughout his career in the Colonial Office he remained on very intimate terms with Lord George Germaine, and generally breakfasted with him. In July, 1778, he was guest of Lord George at Stoneland Lodge, and here, in company with Mr. Ball, the Rector of Withyham, he undertook experiments "to determine the most advantageous situation for the vent in firearms, and to measure the velocities of bullets and the recoil under various circumstances."