The Turtles discover for the first time that they are not the weirdest things in New York when they encounter two villains from the Hidden City pursing a cat-like agent. They have their first encounter with Baron Draxum who is making mutants with the help of his Oozesquitos.

The Turtles look for a way to eliminate New York City's Oozesquito problem.

The Turtles end up facing a new and dangerous threat in their beloved city as Baron Draxum, Huginn, and Muninn gather some of their toughest mutant enemies like Meat Sweats, Hypno-Potamus, Warren Stone, Repo Mantis, and the Sando Brothers in a plot to destroy them.

Splinter and the Turtles must prevent Baron Draxum from getting the final piece of the Kuroi Yōroi.