After defeating a mysterious group of ninjas at the Emeryville Power Station, the Turtles decode part of a map that they were able to liberate from the would-be thieves. Unfortunately, the only words they can make out are: ""EMERYVILLE"" and ""GREEN POWER"". Meanwhile, Vernon at Channel Six News continues to report that it is those ""wretched"" Turtles who are responsible for all the ninja crime occurring throughout the City.
The Turtles rush into action. But before they can make it out of the sewers, they are attacked by Colonel Wesley Knight of the U.S. Armed Forces and his elite group of soldiers, a special unit created to hunt down the TMNT. However, the Turtles escape, proving to be more than Colonel Knight had expected. As they make their getaway, the TMNT see the name: DARK WATER stenciled on Colonel Knight's hi-tech equipment.
April tells the Turtles that Dark Water is a top secret organization, training top commandos and creating super hi-tech military equipment. The TMNT ask her