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, located in northeastern Alphabet City, 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. The above-ground church was an extremely dilapidated structure with its wooden pews in an advanced state of decay and several large holes in the roof. The building was surrounded by a significantly larger green landscaped churchyard, with a concrete foot path leading from the sidewalk to the church's front entrance.
The bunker below 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 East River. It also had a diesel generator, which Donatello was able to repair in order to keep his family supplied with electricity, and various appliances such as a refrigerator and a stove.
The Turtles moved into the bunker, 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 was unwilling to reside at Foot Clan Headquarters. After a brief stint with the Mutanimals at Mutanimals Headquarters, 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.
Mikey threw a Christmas party in the lair during the Christmas Special. Originally intended the be a small gathering of closest friends, the party would become larger when Slash and the Mutanimals (without Old Hob) showed up unannounced. Donnie decorated the exterior of the above-ground church with Christmas lights, and when ready, invited the party-goers outside onto the front churchyard to watch the lights display, which spectacularly lit up the building but accidentally caused a power failure in much of the city around it, coincidentally also cutting power to systems that were being used by the Earth Protection Force at the time to triangulate the Turtles' location. (As if the one well-lit building wasn't enough of a clue.)
In later issues, the portrayal of the above-ground church was inexplicably altered, though the Turtles did not actually move their lair. As recently as issue #90, during Mikey's service for Slash's funeral in the church's chapel, the building still had a front churchyard. But only three issues later in issue #93: City at War, part 1, the church still had signs of greenery next to it, but the front churchyard was completely gone, with the church's front entrance opening directly onto the city sidewalk.
The lair's location was compromised in issue #94: City at War, part 2, when Metalhead betrayed its location to Jonathan Bishop and the Earth Protection Force. As he was showing it to Bishop and his soldiers, he looked through the ground, seeing only Pepperoni sleeping in the lair and no one else home at the time. Given that Metalhead knew the lair was protected by Donatello's security system, Bishop opted not to raid the compound. Neither individual would revisit this location, as Metalhead was deactivated in issue #99: City at War, part 7, and Bishop was killed in issue #100: City at War, part 8, but the EPF continued operating after Bishop's death.
It was not established whether the Turtles intended to keep living in the lair after this, or even whether they knew that the EPF now knew where they lived. After Splinter died in issue #100, in issue #101 they took Splinter's remains to the O'Neil Farm near Northampton, Massachusetts and buried him in the woods nearby. Leonardo, Donatello and Michelangelo started living at the farm instead, and were still living there six months later. Raphael and Pepperoni, however, returned to their neighborhood, which became a part of the newly-designated Mutant Town, where all the human victims of Old Hob's mutagen bomb were forced to live by Mayor Baxter Stockman and the EPF, given that the neighborhood itself had also been contaminated by mutagen fallout. It was not established where Raph was living at this point or whether he still lived in the lair, but he started walking the streets openly as one of countless mutants living in Mutant Town.
- The church's location in Alphabet City is pinpointed on the Zones of Control maps published during the City at War story arc. The location corresponds roughly to the coordinates 40°43'38.41"N, 73°58'34.44"W, which in real life is not an (entirely fictional) abandoned church, but the address of 1 Haven Plaza, located on the east side of Avenue C north of 12th Street and south of 13th Street.
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