Some TMNT stuff really isn't for little kids.
The church is the second New York City lair used by the Turtles and Splinter, after the destruction of their first lair by an invasion of M.O.U.S.E.R.S. robots. The above-ground church itself is not their actual living space, but a Cold-War-era nuclear bomb shelter that was built underneath it in the 1960s to house the church's parishioners in the event of nuclear strike.
This lair first appeared during the Blood Brothers arc, when the Turtles were scouting for a new underground home. They moved in shortly thereafter, and it became their main residence until they were forced to abandon it during the Vengeance arc, when an army of M.O.U.S.E.R.S. and Flyborgs invaded and trashed the bunker. The walls and ceiling were damaged during the attack, but no significant structural weakening seemed to have taken place.
During the Order from Chaos arc, Michelangelo became estranged from his family and unwilling to reside with the Foot Clan. After a brief stint with the Mutanimals, he moved back into the church's bunker and cleaned it up in order to make it livable once again. His brothers later joined him after leaving the Foot Clan, though Splinter did not return to live there.
It was built to potentially house at least fifty people long-term, and consisted of four or five levels, with a sewer access tunnel that led out to the river. It also had a diesel generator, which Donatello was able to repair in order to keep his family supplied with power, and various appliances such as a refrigerator and a stove.
Among the rooms in this lair are:
- a spacious central living room with a few couches in it and a desk
- a secondary living room with a couch and a few armchairs
- an exercise room/armory
- a lab for Donatello
- a kitchen that Michelangelo uses to cook for his family
- four bedrooms for the Turtles, each one decorated and furnished according to his own interests