Some TMNT stuff really isn't for little kids.
First appearing in issue #101 of the IDW continuity, Mutant Town is a quarantined neighborhood on Manhattan's East Side to contain both the newly-mutated victims and the mutagenic fallout of Old Hob's mutagen bomb, which he and Man Ray detonated at New York City Mayor Elect Baxter Stockman's victory celebration in Union Square Park during the preceding City at War arc. Access into and out of Mutant Town is tightly controlled by the Earth Protection Force, which under the recently-deceased Jonathan Bishop had previously instead tried to exterminate every mutant it could find. All mutants discovered outside Mutant Town are detained and relocated there, and all unmutated humans found in Mutant Town are detained and quarantined separately.
Within six months of the mutagen bomb detonation, Mayor Stockman had a high separation barrier constructed around all of Mutant Town to prevent free migration of people in and out of the zone. He claimed that there were plans to provide more aid to Mutant Town's inhabitants, with the goal of eradicating all mutagen contamination, reversing the mutations of the affected, and reunited them with their families.
On the ground, Mutant Town was effectively a ghetto and an increasingly dilapidated slum where many mutants were homeless and scarce food was tightly rationed. To add to their hardships, many of the mutants were also evicted from their homes, rejected by their loved ones, disowned by their families, let go from their jobs, and denied further access to their schools and colleges. A large number of the homeless were children without their parents, many of whom remained human and abandoned their mutant children to their fates. Mutant Town was also patrolled by newly-recruited enforcers of Hob's Mutanimals who were tasked with collecting and controlling access to food. Ostensibly the Mutanimals were rationing this food among the zone's inhabitants, but they did not do so efficiently, effectively behaving more like a criminal gang.
After Clan Hamato drifted apart since Splinter's passing, Raphael alone among the Turtles took permanent residence in Mutant Town where he lives with Pepperoni, and started patrolling the zone as a vigilante. Jennika also periodically visited Mutant Town, covertly commuting between the zone and the O'Neil Farm in Northampton, Massachusetts where the other three Turtles started taking up more permanent residence.
Alopex opened a shelter in Mutant Town, helping the homeless and feeding the hungry with what food was available. Mona Lisa, a recently-mutated human and former physics major at the city college, volunteered to help supply Alopex's shelter with food, which she was actually stealing from the Mutanimals' stocks, which made Mona Lisa a target of Hob's enforcers.
Later when the turtles reunited they deiced to build a Dojo in honor of their father Splinter.
A Zones of Control map in the back of issue #101 clearly shows the boundaries of Mutant Town. It is bounded to the north by 23rd Street, to the west by Park Avenue down to Union Square East then to Broadway, to the south by Houston Street, and to the east by the East River. The zone includes the entire smaller neighborhoods of Alphabet City, the Bowery, the East Village, Little Germany, NoHo, Peter Cooper Village and Stuyvesant Town, and fragments of the Gramercy Park, Little Italy and Nolita. The southeast triangle-shaped portion of Union Square Park is also located in the zone, while the rest of the park lies to the west outside the zone. The church, whose underground bunker had long been home to the Turtles' lair, is also within the zone, located as it is within Alphabet City.
Not located in the zone is the previously established Mutanimals Headquarters, which maps published in previous issues had been shown located in the Lower East Side along the East River facing Brooklyn. The LES is now to the south of Mutant Town, and the issue #101 map no longer showed Mutanimals HQ at all (The Mutanimals now operate within Mutant Town). The zone also included most of the territory of the Purple Dragons, all of which also disappeared from the issue #101 map.