Early churches were often built on top of pre-existing sacred sites, earlier even than the Roman shrine which once stood where the Norman ruins now lie. With the Roman ampitheatre just yards away, this may have been a shrine to Mithras.
A person can only speculate about what may have been here prior to the Roman structure. During the Reformation, St John's received far worse treatment than the nearby, and much bigger, St Werburgh's Cathedral which legend places directly over an ancient Druidic Grove. It seems unlikely that those same Druids would have overlooked this energy-rich focal point.
|Masonic symbolism in St John's the Baptist's Church, Chester.|
More about St John the Baptists's: http://www.parishofchester.com/johns.html