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In the IDW continuity, the Mighty Mutanimals currently have their primary headquarters inside a massive warehouse within Mutant Town. It has been their headquarters since the TMNT #101 story arc.
History[]
During the City at War story arc, without telling the other Mutanimals, their leader Old Hob and his field commander Man Ray carried out a secret plan to detonate a mutagen bomb at the Union Square Park victory celebration of New York City mayor-elect Baxter Stockman. The bomb not only mutated countless humans in the immediate area, but the wind caused mutagen fallout further east across a large swath of Manhattan's East Side, mutating and contaminating those areas, too. In the aftermath, Stockman (who escaped mutation) and the Earth Protection Force corralled the city's new mutant population into the contaminated neighborhoods, at the same time forcibly evacuating all remaining unmutated humans. Stockman had a 50-foot wall built around this new mandatory quarantine zone, which became known as Mutant Town.
At the time, the Mutanimals' headquarters were on the Lower East Side (LES), in an area outside the new quarantine zone. Since it was notionally the Mutanimals' purpose to protect mutants, they relocated to a new headquarters inside Mutant Town, from where they started recruiting countless new members from among the recently-mutated humans. At least some of the recruits, like Puggle and Bandit, also started living there. No longer living here with the Mutanimals were their human scientist Lindsey Baker or longtime members Mondo Gecko or Seymour Gutz; Lindsey as a human was forbidden from being within the new quarantine zone, and Mondo and Seymour had both quit the Mutanimals and left the city in disgust after Hob set off his mutagen bomb.
But unlike the Mutanimals' previous staging grounds at their LES facility or Old Hob's apartment before that, which were stocked with weapons but otherwise maintained an unassuming exterior, their new Mutant Town headquarters became a major well-known factional presence in the community. The building was patrolled by Hob's enforcers wearing new Mutanimals insignia, and it was from where these enforcers started patrolling the surrounding neighborhoods in a haphazard attempt to maintain order.