The wasteland had become a land abundant in greenery merely in the span of a few years after the Beast's fall. It was a result of especially high concentration of Magic Element. As the land is considered eerie and cursed, people usually stay far away from it.
The church was founded by Celica A. Mercury, who became known as Sister. There, she took care of Ragna, Jin and Saya. The church was surrounded by a barrier that prevented anyone from teleporting there, and prevented Yūki Terumi from getting to this place.
On March 1, 2192, Jin received Ice Sword: Yukianesa and the barrier that surrounded the church was lifted, allowing Terumi to use a powerful Magic Formula that caused an explosion, which destroyed the building and put it on fire. Then, Terumi murdered Sister with Jin's assistance, and cut off Ragna's right arm, leaving him to die after Jin wounded him with the blade. Rachel Alucard found Ragna after the fire ended, and guided him to the Black Beast's remains under the church, which replaced his right arm and turned his right eye red. Later, Jūbei took the boy as his apprentice, and taught him fighting and using Magic Formulas.
In Ragna's storyline in BlazBlue: Continuum Shift, there is a flashback in which Jūbei apologizes, supposedly to Celica, saying, "I got [Ragna] involved after all. I'm sorry. I really am. You can hate me if ya want. I promised I'd never use it again, but… I'm just gonna borrow this one more time…". Jūbei is referring to the jacket and sword that Ragna uses, which were retrieved from the church by Jūbei and given to Ragna. They were kept by Celica following Bloodedge's disappearance.
There are numerous points in the storyline, in both BlazBlue: Calamity Trigger and BlazBlue: Continuum Shift, in which characters come back to look at the remains of the church. Jūbei, Rachel, and even Kokonoe herself have visited the site.