In May his wife and her infant joined him at his mother’s home at Woburn. When there, skirmishes took place between the people and troops at Concord, Massachusetts, and Lexington, and in this last fight Major Thompson is said to have taken part with the people; but he was soon the object of ill-feeling, and, although he was saved from immediate arrest by his friend Major Baldwin, a short time afterwards he was arrested, and then he appealed from the Committee of Correspondence of Woburn to the Committee of Safety of the Provincial Congress. When he was acquitted at Woburn and set free, he withdrew his petition from the Committee of Safety. Soon after he was with Major Baldwin at Charlestown, and probably he took part in the battle of Bunker’s Hill. He certainly helped to pack up the library at Cambridge, and was only prevented by the officers of the New Hampshire Militia from obtaining a commission from General Washington. When epaulets were ordered for the non-commissioned officers, he had samples made and sent them with the price to his friend, then Colonel Baldwin, offering to take an order for any number that might be wanted. In August he again writes a long reply to his father-in-law, in answer to letters urging him to express his sorrow that he had done wrong and to ask forgiveness of the people: Woburn, August 14, 1775. As to my being instrumental in the return of some Deserters, by procuring them a pardon, I freely acknowledge that I was. But you will give me leave to say that what I did was done from principles the most unexceptionable--the most disinterested--a sincere desire to serve my _King_ and _Country_, from motives of _Pity_ to those unfortunate Wretches who had deserted the service to which they had _voluntarily_ and so _solemnly_ tyed themselves, and to which they were desirous of returning. If the designed ends were not answered by what I did, I am sincerely and heartily sorry. But if it is a Crime to act from principles like these, I glory in being a Criminal.