The Turtles discover an Atlantean city, not in ancient Greece, but in modern times. After meeting a merman who, in reality is the true King of Atlantis, the Turtles must defeat Shredder & dethrone Bebop, who been set up as a puppet king.

In order to defeat the Turtles, Krang creates 6 clones of himself to deal with them. But, when the clones start to think for themselves & Krang loses control, the Turtles must save the city.