The Turtles must face off against a new enemy, The Rat King, who threatens not only to take control of the city, but of Splinter's mind as well.

Baxter Stockman seeks revenge on Fishface and Dogpound as well as the Turtles, and lures them all into a deadly labyrinth.

Donatello breaks into a secret Kraang detention center in order to rescue Kirby O'Neil, but ends up trapped inside with a deadly prisoner called the Newtralizer.