Four turtles fall into the sewers and are befriended by Hamato Yoshi a Japanese man sent to New York who was forced to live in the sewers. One day he sees a strange green glow which transforms the four turtles into human-like creatures. Hamato (now Master Splinter) changes into a giant rat from the green glow and teaches the turtles the skills of the ninja as they team up with news reporter April O'Neil to battle against Yoshi's arch enemy Shredder and Krang, an alien warlord from Dimension X.

Leonardo, Raphael, Michaelangelo and Donatello must save New York City from the evil crime lord Shredder and his assistant, Baxter Stockman. The Turtles must fight foot soldiers, mice, and gangs and get help from their sensei Splinter, her friend April O'Neil, and her partner Casey Jones in an action-packed new series.

When the Teenage Mutant Ninja Turtles acquire Mutastones from Crys-Mu, the spirit of light, they acquire the ability to enhance themselves into Super Turtles for a duration of three minutes. Meanwhile, the evil Shredder and his minions Bebop and Rocksteady stumble upon the Dark Mutastone, which transforms them into Devil Shredder, Supermutant Bebop and Supermutant Rocksteady, respectively. But the Turtles have one more trick up their shells: all four of them can combine into their ultimate form—Turtle Saint.