The Gotham Cathedral was built in 1790 by the pseudo-immortal Mister Whisper, who designed the place using Gothic architecture to imbue it with magical properties so it could act as a soul trap on a massive scale. His ultimate plan was to release a deadly plague through the Cathedral's glass that would contaminate and kill most of Gotham's population, but he had to wait hundreds of years to accomplish this. When the time came, Mr. Whisper was stopped by Batman and the plague was removed from the Cathedral by the authorities of the city.
The Gotham Cathedral was the chosen place for the final confrontation between Batman and the Joker. The place was abandoned at the time and in the aftermath of the struggle, several parts of the building were damaged like the belltower, some statues and the main entrance, due to the crashing of the Batwing.