The church was where Robert Newman lit a signal to warn of incoming British troops, which would later give rise to the famous phrase "one if by land, and two if by sea". This phrase was related to Paul Revere's midnight ride of 18 April 1775 that preceded the Battles of Lexington and Concord which started the American Revolutionary War.
After the war, U.S. President George Washington and the Assassin Connor witnessed a vision of an alternate timeline through the Apple of Eden. In it, Washington, seduced by the Apple, became a tyrannical and evil king. Under the Apple's influence, Benjamin Franklin had the church burned to the ground with dozens of innocents inside it, an act which horrified him but which he was unable to stop on his own. When Connor freed Franklin, Samuel Adams brought up this atrocity and very nearly had the man shot for it.