The plot for season 1 of Tmnt is thew four turtles come of hiding in the sewers and discover the kraang. They see them kidnapping kirby and april o'neil. The turtles ally themselves with april to save her dad. They fought the shredder for the first time and almost died. Shredder was no joke. Leo then comes across karai (shredder's daughter) and fall for her. They found out that the kraang and shredder were working together to get what they both want. The season ends with leonardo's victory of the kraang's defeatand splinter knowing that karai is his daughter.

For season 2 the turtles celebrate their victory, but comes a bigger problem. Mutagen falls from the sky and crashes onto the ground and is turning everyone into mutants, including april's dad who got mutated into a vampire bat. Then april blames the turtles for her father's mutation, and leaves. She meets casey jones and they were together. Donnie gets jealous of casey for stealing his girl. The raph meets casey and they both fought each other. But after they stopped and footbot they became best friends. Meanwhile, shredder returned from his trip to japan with his new second-in-command, Tigerclaw. While that was happening karai was able to get into the turtles hideout and finds out the truth about her mother, and that splinter is her true father. With so much hatred over shredder, Karai goes after the shredder for revenge and gets captured. Then she gets dunked into the mutagen and turns into a horned viper. After that the kraang had perfected the mutagen and started there invasion, wehile the shredder was going after splinter and Leonardo. Leonardo battled shredder's army successfully, but gets badly wounded by the shredder. Now the turtles, april, and casey drove away from the battle and went to the farm house up north.

The turtles retreated to april's farm house and leo woke up from his coma in three months trying to recover. The turtles went on so many adventures at the farm house with defeating the creep, meeting bigfoot, stopping the speed demon, and befriending an army of toads. Leo discovers that they were being lazy and not training as much, so he claims that they should have a three day camping trip, only turtles. During their camping trip splinter's spirit appears in the fire and tells the turtles to go on separate journeys to sface their greatest problems. They suceeded there mission and headed back to new york. Then the turtles find spinter and make a new hideout at a pizza place. Donnie makes a batch of retro mutagen with the help of mikey and saved the citizens of New York. While that was happening shredder send out his new henchmen Bebop and Rocksteady to find Karai and to change her back. Then they discovered a time-traveller , Renet who sends the turtles back in time to where splinter and shredder are. They meet tang shen and she tells them everything they know about the feud between Splinter and shredder. After that a new alien species, the triceratons are invading earth to kill the kraang, which results the triceratons destroying earth. The turtles, april and casey go on a fugitoid ship and escape from the destruction of earth.

The turtles, april and casey meet professor honeycutt AKA the fugitoid and travel into space to find the pieces to stop the triceratons from using the heart of darkness. They travel into space and made new enemies Lord dregg and armaggon. Raphael also found his girlfriend Mona lisa, who is an extraterrestrial salamander. They were also able to meet there counterparts from 1987 and stopped kraang 1987 from wiping out their dimesion. 6 months had past and the triceratons have all the pieces to the heart of darkness. The turtles and their allies defeated the triceratons and stopped the heart of darkness, and splinter had hurt the shredder pretty badly and won the war. Then april was announced as a kunoichi to the turtles and karai's best friend shinigami moved to new york from Japan. Meanwhile the shredder was doing an experiment to help him regain his strength. The shredder was now mutated to super shredder and killed splinter. The turtles come up with a plan to defeat the shredder once and for all. During the battle, Leonardo decapitated the shredder and finished him. The turtles destroyed shredder's army and lived in peace in New York.

After the shredder's defeat, Tigerclaw was trying to resurrect the him with the help of kavaxas. They need shredder head and heart to resurrect him. The turtles try to stop him from bringing the shredder back form the dead, but they were too late and kavaxas was free from the stone that controls him. Michelangelo was able to fix the stone and save the city from kavaxas's rage. Afterwards, the Turtles face different challenges like the return of Lord Dregg when he collaborates with Newtralizer, being transported to Miyamoto Usagi's reality where they help to protect the pug Kintaro from the evil gray wolf Jei, an adventure featuring an alternate future ruled by mutant animals, and another adventure involving the return of Savanti Romero where he collaborates with Count Dracula to make Earth more habitable for monsters. Then Bebop and rocksteady were allied with 1987 shredder and kraang to destroy the world. The turtles have help from their counterparts to help defeat the shredder and Kraang 1987. They stopped their plan with the help of bebop and rocksteady and send them back to their dimesion. After that, a major catastrophe as Raphael traverses a wasteland Earth, along with Donatello (whose consciousness is transferred into a robot). They eventually encounter Michaelangelo (who has become a hippie guru, "The Holy Chalupa") and finally Leonardo, who had lost his memory and sanity and mutated into the archvillain Maximus Kong, before Raphael is finally able to re-trigger Leonardo's consciousness, reuniting the four core characters for a bittersweet happy ending.