However, early in the American Revolution, Church was also sending secret information to General Thomas Gage, the British commander, and when one of his letters into Boston was intercepted, he was tried and convicted of "communicating with the enemy".

His great-grandfather,[2] Colonel Benjamin Church, took a prominent part in the war with the Narragansett Indians and led the force which hunted King Philip to his death on August 12, 1676.

In 1774, Church was elected a delegate to the Massachusetts Provincial Congress and later made a member of its Committee of Safety, which was in charge of preparing for armed conflict.

Colleagues noted, however, that he had insisted on entering Boston soon after the Battle of Lexington and Concord, and while there he was seen in conference with British General Thomas Gage; he claimed to have been arrested and released.

In the meantime, on July 2, General George Washington had arrived at Cambridge to take command of the colonial forces, and Church was one of the committee appointed to receive him.

In his own defense, Church complained that rivals were jealous of his position and reportedly asked for permission to leave the Army.

When two teams of gentlemen decoded it, they found it contained an account of the American forces before Boston, though no disclosures of great importance.

The matter was placed before a court of inquiry made up of general officers, Washington presiding, to whom Church admitted the authorship of the letter, but explained that it was written with the object of impressing the enemy with the strength and position of the colonial forces in order to prevent an attack while the Continental army was still short of ammunition and in hopes of aiding to bring about an end to hostilities.

The court considered that Church had carried on a criminal correspondence with the enemy and recommended that the matter be referred to the Continental Congress for its action.

The report of Washington to the President of Congress stated: I have now a painful though necessary duty to perform, respecting Doctor Church, the Director of the Hospital.

Despite an eloquent appeal in his own defense, he was unanimously expelled as a member of the House due to other "coded documents" of his being found in the trial proceedings that Congress regarded as proving his guilt.

[7] The Continental Congress on October 17, 1775, elected John Morgan "in the room of" Church, and on November 7 passed the following resolution: That Doctor Church be close confined in some secure jail in the Colony of Connecticut, without use of pen, ink and paper, and that no person be allowed to converse with him except in the presence and hearing of a magistrate of the town or the sheriff of the county where he is confined, and in the English language, until further orders from this or a future Congress.

[8] When scholars were able to open General Gage's files early in the 20th century, they discovered earlier letters with significant intelligence about the American forces that could only have come from Church.