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In the IDW continuity, for a time, the Mighty Mutanimals had their primary headquarters in an abandoned building in Manhattan's Lower East Side (LES) by the East River.
History[]
In the Monsters, Misfits, and Madmen story arc, the group of mutants that would become the Mutanimals—then comprising just Old Hob, Slash and Pigeon Pete—were living in Old Hob's apartment. When Hob recruited human former StockGen scientist Lindsey Baker to create a mutant army for him, Lindsey insisted that the apartment was inadequate for use as a proper library.
In the Teenage Mutant Ninja Turtles: Mutanimals miniseries, the Mutanimals now appeared to be living in at their new headquarters on the LES, where it was home to Hob, Slash, Pete and Lindsey as well as Lindsey's recently-produced mutants Herman the Hermit Crab and Mondo Gecko, which she had changed with a combination of mutagen and the recently rediscovered psychotropic compound. By the end of the miniseries, liberated Null Group mutants Seymour Gutz, Man Ray and Sally Pride were also living there.
The Mutanimals were still living here in the Order from Chaos story arc when Michelangelo was briefly invited to join them, but Mikey didn't stay for long as the discovery of Hob's secret weapons warehouse disgusted both Slash and Mikey into leaving the Mutanimals.
Except during the Desperate Measures story arc when all Mutanimals domestic scenes were shown taking place in a different building's apartment, apparently belonging to Hob, the Mutanimals were shown living and operating primarily out of their LES headquarters until the end of the City at War story arc. In this arc, without telling the other Mutanimals, Hob and Ray had secretly planned to detonate a mutagen bomb at the Union Square Park victory celebration of New York City mayor-elect Baxter Stockman. Countless random humans in the area immediately mutated, the Turtles, Mutanimals and Angel Bridge had no choice but to gather as many mutants from the immediately surrounding area into the Mutanimals' Triceraton drop ship and evacuate them to Mutanimals HQ before the dangerously unhinged Jonathan Bishop could start trying to kill them all.
Their stay there would not last, as Stockman and the Earth Protection Force (now minus the recently-deceased Bishop) were provoked into rounding up every mutant they could find in the city and corral them into the areas of Manhattan's East Side most contaminated with mutagen fallout and built a 50-foot wall around them, while all unmutated human residents within the area were forcibly evacuated and quarantined separately. This all-mutant quarantine zone became known as Mutant Town. Since it was notionally the Mutanimals' purpose to protect mutants, they relocated their primary operations to a new warehouse building located within Mutant Town.
Gallery[]
Trivia[]

Mutanimals Headquarters' location on the LES is marked on the Zones of Control maps published during the City at War story arc. Its coordinates are roughly 40°42'36.23"N, 73°59'2.37"W, near the waterfront just southeast of the intersection of South Street and Avenue C. In real life, these coordinates correspond to a parking lot just east of Pier 36 New York, an event venue.