The mutagen bomb's fallout continues to affect NYC in increasingly disturbing ways. As the government struggles to come to grips with a growing humanitarian crisis, mutants start to go missing. The TMNT trace the clues to the waterfront and find something terrifying that is now living in the depths!

Meanwhile, a falling out between Baxter and April could have dire consequences for Mutant Town, where life has changed forever. But life somehow finds a way to move forward and in a stand alone story that delves deeper into the denizens of Mutant Town follow three-interconnected stories as the TMNT immerse themselves in their new home.