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Welcome to the new world of TMNT! After the cataclysmic events of TMNT #100, the Turtles find New York City drastically changed-new factions and enemies are on the rise, and allies are in short supply. The Turtles discover that in order to survive they will need to work together like never before!
In just one scene, at Splinter's funeral, Donatello's prosthetic carapace has an unexplained different appearance from its usual realistic exterior (as Zayton Honeycutt had originally crafted it), with a pronounced metallic grey color and visible bolts. But in later scenes in this same issue, his carapace again appears as it previously had.
For the first time, other Turtles besides Jennika are shown fully clothed even in private, with the exception of Michelangelo who after the six-month time skip is only shown in one scene, lying in bed. In previous wintertime stories (like Michelangelo macro-series issue and issue #89), the four Turtles had worn arm and leg warmers resembling thigh stockings and opera gloves, but now they wear trousers, and Leonardo and Donatello also wear outfit tops they hadn't previously normally worn. Another animal-born mutant in Mutant Town, Alopex, does not appear to have started wearing bottoms, but the cloth of her top appears to drape adequately over her bottom front. The Turtles' appearance of body modesty (or lack thereof) was brought up before in the miniseries Teenage Mutant Ninja Turtles/Ghostbusters 2, where, while visiting Zoo Amsterdam, Peter Venkman had Mikey put on Venkman's outer clothes before being seen publicly in a city of otherwise fully-dressed anthropomorphs. With Mutant Town also being home to a large population of human-born mutants, they also wear clothes much the same as they did as unmutated humans, which make the Turtles' usual outfits (or lack thereof) appear immodestly underdressed by the contemporary standards of human New Yorkers.
Raphael addresses Alopex as "Al," which is the first time in the IDW continuity that she's been referred to by this nickname. But "Al" was long already the more common nickname for the version of Alopex appearing in Sophie Campbell's TMNT fan webcomic Secrets of the Ooze.
Jennika comments that Raphael is like her "horrible kid brother." The topic of Jenny's age relative to the other four Turtles is a complicated one, as on one hand their physical turtle bodies are only a few years old, but they are reincarnated humans who were born centuries before in feudal Japan. But since the Hamato Sons died as teenagers and reincarnated socially still teenagers, this may imply that Jenny's age is chronologically older than the social age of at least Raph and his socially younger brothers Donatello and Michelangelo. (Leonardo is socially older than Raph, which would make his social age unclear in relation to Jenny.)