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Baxter Stockman & his alien computer return to Earth from the Dimensional Limbo & take possession of Shredder's Retro-Mutagen Ray Gun.
Kerma the space turtle returns once again for the Turtles help in programming his city's new defence robots but Groundchuck and Dirtbag have also returned to the city to cause trouble.
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.