In 1775 Ely, after the news of the battle of Lexington came to Westport, mustered a company of militia as Captain and marched with it to Roxbury, now part of Boston. The next year as Major he performed a tour of duty as commandant at Fort Trumbull, New London, also serving there as physician and one day he sent a "pithy" letter to the Captain of a vessel at the mouth of the harbor suspected of being English which promptly sailed away.